Mass spectrometric methods for biomolecular screening

ABSTRACT

The present invention provides methods for the determination of the structure of biomolecular targets, as well as the site and nature of the interaction between ligands and biomolecular targets. The present invention also provides methods for the determination of the relative affinity of a ligand for the biomolecular target it interacts with. Also provided are methods for screening ligand or combinatorial libraries of compounds against one or more than one biological target molecules. The methods of the invention also allow determination of the relative binding affinity of combinatorial and other compounds for a biomolecular target. The present invention further provides methods for the use of mass modifying tags for screening multiple biomolecular targets. In a preferred embodiment, ligands which have great specificity and affinity for molecular interaction sites on biomolecules, especially RNA can be identified. In preferred embodiments, such identification can be made simultaneously with libraries of ligands.

CROSS-REFERENCE TO RELATED APPLICATIONS

This application is a continuation of application Ser. No. 09/260,310filed Mar. 2, 1999, now U.S. Pat. No. 6,329,146, which is aContinuation-In-Part of U.S. patent application Ser. No. 09/076,206filed May 12, 1998, and Provisional Application Ser. No. 60/076,534,filed Mar. 2, 1998, the disclosures of which are incorporated herein byreference in their entirety.

FIELD OF THE INVENTION

The present invention is directed to methods for the use of massspectrometry for the determination of the structure of a biomoleculeespecially a nucleic acid target, the site(s) of interaction betweenligands and the target, the relative binding affinity of ligands for thetarget and other useful information. The present invention also providesmethods for the use of mass spectrometry for screening chemical mixturesor libraries, especially combinatorial libraries, for individualcompounds that bind to a selected target and can be used inpharmaceuticals, veterinary drugs, agricultural chemicals industrialchemicals and otherwise. The present invention is further directed tomethods for screening multiple targets simultaneously against, e.g. acombinatorial library of compounds. A further aspect of the inventionprovides methods for determining the interaction between one or aplurality of molecular species, especially “small”molecules and amolecular interaction site on a nucleic acid, especially an RNA.

BACKGROUND OF THE INVENTION

The process of drug discovery is changing at a fast pace because of therapid progress and evolution of a number of technologies that impactthis process. Drug discovery has evolved from what was, several decadesago, essentially random screening of natural products, into a scientificprocess that not only includes the rational and combinatorial design oflarge numbers of synthetic molecules as potential bioactive agents, suchas ligands, agonists, antagonists, and inhibitors, but also theidentification, and mechanistic and structural characterization of theirbiological targets, which may be polypeptides, proteins, or nucleicacids. These key areas of drug design and structural biology are oftremendous importance to the understanding and treatment of disease.However, significant hurdles need to be overcome when trying to identifyor develop high affinity ligands for a particular biological target.These include the difficulty surrounding the task of elucidating thestructure of targets and targets to which other molecules may be boundor associated, the large numbers of compounds that need to be screenedin order to generate new leads or to optimize existing leads, the needto dissect structural similarities and dissimilarities between theselarge numbers of compounds, correlating structural features to activityand binding affinity, and the fact that small structural changes canlead to large effects on biological activities of compounds.

Traditionally, drug discovery and optimization have involved theexpensive and time-consuming, and therefore slow, process of synthesisand evaluation of single compounds bearing incremental structuralchanges. When using natural products, the individual components ofextracts had to be painstakingly separated into pure constituentcompounds prior to biological evaluation. Further, all compounds had tobe carefully analyzed and characterized prior to in vitro screening.These screens typically included evaluation of candidate compounds forbinding affinity to their target, competition for the ligand bindingsite, or efficacy at the target as determined via inhibition, cellproliferation, activation or antagonism end points. Considering allthese facets of drug design and screening that slow the process of drugdiscovery, a number of approaches to alleviate or remedy these matters,have been implemented by those involved in discovery efforts.

One way in which the drug discovery process is being accelerated is bythe generation of large collections, libraries, or arrays of compounds.The strategy of discovery has moved from selection of drug leads fromamong compounds that are individually synthesized and tested to thescreening of large collections of compounds. These collections may befrom natural sources (Sternberg et al., Proc. Natl. Acad. Sci. USA,1995, 92, 1609-1613) or generated by synthetic methods such ascombinatorial chemistry (Ecker and Crooke, Bio/Technology, 1995, 13,351-360 and U.S. Pat. No. 5,571,902, incorporated herein by reference).These collections of compounds may be generated as libraries ofindividual, well-characterized compounds synthesized, e.g. via highthroughput, parallel synthesis or as a mixture or a pool of up toseveral hundred or even several thousand molecules synthesized bysplit-mix or other combinatorial methods. Screening of suchcombinatorial libraries has usually involved a binding assay todetermine the extent of ligand-receptor interaction (Chu et al., J. Am.Chem. Soc., 1996, 118, 7827-35). Often the ligand or the target receptoris immobilized onto a surface such as a polymer bead or plate. Followingdetection of a binding event, the ligand is released and identified.However, solid phase screening assays can be rendered difficult bynon-specific interactions.

Whether screening of combinatorial libraries is performed viasolid-phase, solution methods or otherwise, it can be a challenge toidentify those components of the library that bind to the target in arapid and effective manner and which, hence, are of greatest interest.This is a process that needs to be improved to achieve ease andeffectiveness in combinatorial and other drug discovery processes.Several approaches to facilitating the understanding of the structure ofbiopolymeric and other therapeutic targets have also been developed soas to accelerate the process of drug discovery and development. Theseinclude the sequencing of proteins and nucleic acids (Smith, in ProteinSequencing Protocols, Humana Press, Totowa, N.J., 1997; Findlay andGeisow, in Protein Sequencing: A Practical Approach, IRL Press, Oxford,1989; Brown, in DNA Sequencing, IRL Oxford University Press, Oxford,1994; Adams, Fields and Venter, in Automated DNA Sequencing andAnalysis, Academic Press, San Diego, 1994). These also includeelucidating the secondary and tertiary structures of such biopolymersvia NMR (Jefson, Ann. Rep. in Med. Chem., 1988, 23, 275; Erikson andFesik, 30 Ann. Rep. in Med. Chem., 1992, 27, 271-289), X-raycrystallography (Erikson and Fesik, Ann. Rep. in Med. Chem., 1992, 27,271-289) and the use of computer algorithms to attempt the prediction ofprotein folding (Copeland, in Methods of Protein Analysis: A PracticalGuide to Laboratory Protocols, Chapman and Hall, New York, 1994;Creighton, in Protein Folding, W. H. Freeman and Co., 1992). Experimentssuch as ELISA (Kemeny and Challacombe, in ELISA and other Solid PhaseImmunoassays: Theoretical and Practical Aspects; Wiley, New York, 1988)and radioligand binding assays (Berson and Yalow, Clin. Chim. Acta,1968, 22, 51-60; Chard, in “An Introduction to Radioimmunoassay andRelated Techniques,” Elsevier press, Amsterdam/New York, 1982), the useof surface-plasmon resonance (Karlsson, Michaelsson and Mattson, J.Immunol. Methods, 1991, 145, 229; Jonsson et al., Biotechniques, 1991,11, 620), and scintillation proximity assays (Udenfriend, Gerber andNelson, Anal. Biochem., 1987, 161, 494-500) are being used to understandthe nature of the receptor-ligand interaction.

All of the foregoing paradigms and techniques are now available topersons of ordinary skill in the art and their understanding and masteryis assumed herein.

Likewise, advances have occurred in the chemical synthesis of compoundsfor high-throughput biological screening. Combinatorial chemistry,computational chemistry, and the synthesis of large collections ofmixtures of compounds or of individual compounds have all facilitatedthe rapid synthesis of large numbers of compounds for in vitroscreening. Despite these advances, the process of drug discovery andoptimization entails a sequence of difficult steps. This process canalso be an expensive one because of the costs involved at each stage andthe need to screen large numbers of individual compounds. Moreover, thestructural features of target receptors can be elusive.

One step in the identification of bioactive compounds involves thedetermination of binding affinity of test compounds for a desiredbiopolymeric or other receptor, such as a specific protein or nucleicacid or combination thereof. For combinatorial chemistry, with itsability to synthesize, or isolate from natural sources, large numbers ofcompounds for in vitro biological screening, this challenge ismagnified. Since combinatorial chemistry generates large numbers ofcompounds or natural products, often isolated as mixtures, there is aneed for methods which allow rapid determination of those members of thelibrary or mixture that are most active or which bind with the highestaffinity to a receptor target.

From a related perspective, there are available to the drug discoveryscientist a number of tools and techniques for the structuralelucidation of biologically interesting targets, for the determinationof the strength and stoichiometry of target-ligand interactions, and forthe determination of active components of combinatorial mixtures.

Techniques and instrumentation are available for the sequencing ofbiological targets such as proteins and nucleic acids (e.g. Smith, inProtein Sequencing Protocols, 1997 and Findlay and Geisow, in ProteinSequencing: A Practical Approach, 1989) cited previously. While thesetechniques are useful, there are some classes and structures ofbiopolymeric target that are not susceptible to such sequencing efforts,and, in any event, greater convenience and economy have been sought.Another drawback of present sequencing techniques is their inability toreveal anything more than the primary structure, or sequence, of thetarget.

While X-ray crystallography is a very powerful technique that can allowfor the determination of some secondary and tertiary structure ofbiopolymeric targets (Erikson and Fesik, Ann. Rep. in Med. Chem., 1992,27, 271-289), this technique can be an expensive procedure and verydifficult to accomplish. Crystallization of biopolymers is extremelychallenging, difficult to perform at adequate resolution, and is oftenconsidered to be as much an art as a science. Further confounding theutility of X-ray crystal structures in the drug discovery process is theinability of crystallography to reveal insights into the solution-phase,and therefore the biologically relevant, structures of the targets ofinterest.

Some analysis of the nature and strength of interaction between a ligand(agonist, antagonist, or inhibitor) and its target can be performed byELISA (Kemeny and Challacombe, in ELISA and other Solid PhaseImmunoassays: 1988), radioligand binding assays (Berson and Yalow, Clin.1968, Chard, in “An Introduction to Radioimmunoassay and RelatedTechniques,” 1982), surface-plasmon resonance (Karlsson, Michaelsson andMattson, 1991, Jonsson et al., Biotechniques, 1991), or scintillationproximity assays (Udenfriend, Gerber and Nelson, Anal. Biochem., 1987),all cited previously. The radioligand binding assays are typicallyuseful only when assessing the competitive binding of the unknown at thebiding site for that of the radioligand and also require the use ofradioactivity. The surface-plasmon resonance technique is morestraightforward to use, but is also quite costly. Conventionalbiochemical assays of binding kinetics, and dissociation and associationconstants are also helpful in elucidating the nature of thetarget-ligand interactions.

When screening combinatorial mixtures of compounds, the drug discoveryscientist will conventionally identify an active pool, deconvolute itinto its individual members via resynthesis, and identify the activemembers via analysis of the discrete compounds. Current techniques andprotocols for the study of combinatorial libraries against a variety ofbiologically relevant targets have many shortcomings. The tediousnature, high cost, multi-step character, and low sensitivity of many ofthe above-mentioned screening technologies are shortcomings of thecurrently available tools. Further, available techniques do not alwaysafford the most relevant structural information—the structure of atarget in solution, for example. Instead they provide insights intotarget structures that may only exist in the solid phase. Also, the needfor customized reagents and experiments for specific tasks is achallenge for the practice of current drug discovery and screeningtechnologies. Current methods also fail to provide a convenient solutionto the need for deconvolution and identification of active members oflibraries without having to perform tedious re-syntheses and re-analysesof discrete members of pools or mixtures.

Therefore, methods for the screening and identification of complexchemical libraries especially combinatorial libraries are greatly neededsuch that one or more of the structures of both the target and ligand,the site of interaction between the target and ligand, and the strengthof the target-ligand interaction can be determined. Further, in order toaccelerate drug discovery, new methods of screening combinatoriallibraries are needed to provide ways for the direct identification ofthe bioactive members from a mixture and to allow for the screening ofmultiple biomolecular targets in a single procedure. Straightforwardmethods that allow selective and controlled cleavage of biopolymers,while also analyzing the various fragments to provide structuralinformation, would be of significant value to those involved inbiochemistry and drug discovery and have long been desired. Also, it ispreferred that the methods not be restricted to one type of biomoleculartarget, but instead be applicable to a variety of targets such asnucleic acids, peptides, proteins and oligosaccharides.

OBJECTS OF THE INVENTION

A principal object of the present invention is to provide novel methodsfor the determination of the structure of biomolecular targets andligands that interact with them and to ascertain the nature and sites ofsuch interactions.

A further object of the invention is to determine the structuralfeatures of biomolecular targets such as peptides, proteins,oligonucleotides, and nucleic acids such as the primary sequence, thesecondary and folded structures of biopolymers, and higher ordertertiary and quaternary structures of biomolecules that result fromintramolecular and intermolecular interactions.

Yet another object of the invention is to determine the site(s) andnature of interaction between a biomolecular target and a binding ligandor ligands. The binding ligand may be a “small” molecule, a biomoleculesuch as a peptide, oligonucleotide or oligosaccharide, a naturalproduct, or a member of a combinatorial library.

A further object of the invention is to determine the relative bindingaffinity or dissociation constant of ligands that bind to biopolymertargets. Preferably, this gives rise to a determination of relativebinding affinities between a biopolymer such as an RNA/DNA target andligands e.g. members of combinatorially synthesized libraries.

A further object of the invention is to determine the absolute bindingaffinity or dissociation constant of ligands that bind to biopolymertargets.

A still further object of the present invention is to provide a generalmethod for the screening of combinatorial libraries comprisingindividual compounds or mixtures of compounds against a biomoleculartarget such as a nucleic acid, so as to determine which components ofthe library bind to the target.

An additional object of the present invention is to provide methods forthe determination of the molecular weight and structure of those membersof a combinatorial library that bind to a biomolecular target.

Yet another object of the invention is to provide methods for screeningmultiple targets such as nucleic acids, proteins, and other biomoleculesand oligomers simultaneously against a combinatorial library ofcompounds.

A still further object of the invention is to ascertain the specificityand affinity of compounds, especially “small” organic molecules to bindto or interact with molecular interaction sites of biological molecules,especially nucleic acids such as RNA. Such molecules may be andpreferably do form ranked hierarchies of ligands and potential ligandsfor the molecular interaction sites, ranked in accordance with predictedor calculated likelihood of interaction with such sites.

Another object of the present invention is to alleviate the problem ofpeak overlap in mass spectra generated from the analysis of mixtures ofscreening targets and combinatorial or other mixtures of compounds. In apreferred embodiment, the invention provides methods to solve theproblems of mass redundancy in combinatorial or other mixtures ofcompounds, and also provides methods to solve the problem of massredundancy in the mixture of targets being screened.

A further object of the invention is to provide methods for determiningthe binding specificity of a ligand for a target in comparison to acontrol. The present invention facilitates the determination ofselectivity, the identification of non-specific effects and theelimination of non-specific ligands from further consideration for drugdiscovery efforts.

The present invention provides, inter alia, a series of new methods andapplications for the determination of the structure and nature ofbinding of ligands to a wide variety of biomolecular targets. This newapproach provides structural information for screening combinatoriallibraries for drug lead discovery.

SUMMARY OF THE INVENTION

One aspect of the invention is a method to determine the structure ofbiomolecular targets such as nucleic acids using mass spectrometry. Themethod provides not only the primary, sequence structure of nucleic acidtargets, but also information about the secondary and tertiary structureof nucleic acids, RNA and DNA, including mismatched base pairs, loops,bulges, kinks, and stem structures. This can be accomplished inaccordance with one embodiment by incorporating deoxynucleotide residuesor other modified residues into an oligoribonucleotide at specific sitesfollowed by selective cleavage of these hybrid RNA/DNA nucleic acids ina mass spectrometer. It has now been found that electrospray ionizationof the nucleic acid, cleavage of the nucleic acid, and subsequent tandemMS^(n) spectrometry affords a pattern of fragments that is indicative ofthe nucleic acid sequence and structure. Cleavage is dependent on thesites of incorporation of the deoxynucleotide or other foreign residuesand the secondary structure of the nucleic acid. This method thereforeprovides mass spectral data that identifies the sites and types ofsecondary structure present in the sequence of nucleic acids.

When the present methods are performed on a mixture of the biomoleculartarget and a ligand or molecule that binds to the target, it is possibleto ascertain both the extent of interaction and the location of thisinteraction between ligand and biomolecule. The binding of the ligand tothe biomolecule protects the binding site on the biomolecule from facilecleavage during mass spectrometry. Therefore, comparison of ESI-MS^(n)mass spectra generated, using this method, for RNA/DNA in the presenceand the absence of a binding ligand or drug reveals the location ofbinding. This altered cleavage pattern is clearly discerned in the massspectrum and correlated to the sequence and structure of the nucleicacid. Thus, the absolute binding affinity of the test ligand can bedetermined by the methods of the present invention. Comparison of theabundance of the nucleic acid-ligand noncovalent complex ion to theabundance of a similar complex ion generated from a standard compound(such as paromomycin for the 16S RNA A site) whose binding affinity isknown, allows for the determination of relative binding affinity of thetest ligand.

The methods of this invention can be used for the rapid screening oflarge collections of compounds. It is also possible to screen mixturesof large numbers-of compounds that are generated via combinatorial orother means. When a large mixture of compounds is exposed to abiomolecular target, such as a nucleic acid, a small fraction of ligandsmay exhibit some binding affinity to the nucleic acid. The actual numberof ligands that may be detected as binders is based on the concentrationof the nucleic acid target, the relative concentrations of thecomponents of the combinatorial mixture, and the absolute and relativebinding affinities of these components. The method is capable ofseparating different noncovalent complexes, using techniques such asselective ion trapping, or accumulation and analyzing each complex forthe structure and identity of the bound ligand using collisionallyactivated dissociation or MS^(n) experiments. The methods of thisinvention, therefore, can not only serve as methods to screencombinatorial libraries for molecules that bind to biomolecular targets,but can also provide, in a straightforward manner, the structuralidentity of the bound ligands. In this manner, any mass redundancy inthe combinatorial library does not pose a problem, as the methods canprovide high resolution molecular masses and also able to discerndifferences between the different structures of ligands of identicalmolecular mass using tandem methods.

In accordance with preferred embodiments, a target biomolecule such asan RNA having a molecular interaction site, is presented with one ormore ligands or suspected ligands for the interaction site underconditions such that interaction or binding of the ligand to themolecular interaction site can occur. The resulting complex, which maybe of one or even hundreds of individual complexes of ligands with theRNA or other biomolecule, is then subjected to mass spectrometricevaluation in accordance with the invention. “Preparative” massspectrometry can isolate individual complexes which can then befragmented under controlled conditions within the mass spectrometricenvironment for subsequent analysis. In this way, the nature and degree,or absolute binding affinity, of binding of the ligands to the molecularinteraction site can be ascertained. Identification of specific, strongbinding ligands can be made and those selected for use either astherapeutics, agricultural, industrial or other chemicals, or the sameused as lead compounds for subsequent modification into improved formsfor such uses.

A further application of the present invention is the use of massspectrometric methods for the simultaneous screening of multiplebiomolecular targets against combinatorial libraries or mixtures ofcompounds. This rather complex screening procedure is made possible bythe combined power of the mass spectrometric methods used and the way inwhich the screening is performed. When screening multiple target nucleicacids, for example, mass redundancy is a concern, especially if two ormore targets are of similar sequence composition or mass. This problemis alleviated by the present invention, by using special mass modifying,molecular weight tags on the different nucleic acid targets beingstudied. These mass modifying tags are typically large molecular weight,non-ionic polymers including but not limited to, polyethylene glycols,polyacrylamides and dextrans, that are available in many different sizesand weights, and which may be attached at one or more of many differentpossible sites on nucleic acids. Thus similar nucleic acid targets maybe differentially tagged and now be readily differentiated, in the massspectrum, from one another by their distinctly different mass to chargeratios (m/z signals). Using the methods of this invention, screeningefforts can be significantly accelerated because multiple targets cannow be screened simultaneously against mixtures of large numbers ofcompounds.

Another related advantage of the methods of this invention is theability to determine the specificity of binding interactions between anew ligand and a biomolecular target. By simultaneously screening atarget nucleic acid, for example, and one or more control nucleic acidsagainst a combinatorial library or a specific ligand, it is possible toascertain, using the methods of this invention, whether the ligand bindsspecifically to only the target nucleic acids, or whether the bindingobserved with the target is reproduced with control nucleic acids and istherefore non-specific.

The methods of the invention are applicable to the study of a widevariety of biomolecular targets that include, but are not limited to,peptides, proteins, receptors, antibodies, oligonucleotides, RNA, DNA,RNA/DNA hybrids, nucleic acids, oligosaccharides, carbohydrates, andglycopeptides. The molecules that may be screened by using the methodsof this invention include, but are not limited to, organic or inorganic,small to large molecular weight individual compounds, mixtures andcombinatorial libraries of ligands, inhibitors, agonists, antagonists,substrates, and biopolymers, such as peptides, nucleic acids oroligonucleotides. The mass spectrometric techniques which can be used inthe methods of the invention include, but are not limited to, MS^(n),collisionally activated dissociation (CAD) and collisionally induceddissociation (CID) and infrared multiphoton dissociation (IRMPD). Avariety of ionization techniques may be used including, but not limitedto, electrospray, MALDI and FAB. The mass detectors used in the methodsof this invention include, but are not limited to, FTICR, ion trap,quadrupole, magnetic sector, time of flight (TOF), Q-TOF, and triplequadrupole. The methods of this invention may also use “hyphenated”techniques such as, but not limited to, LC/MS and CE/MS, all asdescribed more fully hereinafter.

BRIEF DESCRIPTION OF THE DRAWINGS

FIG. 1 shows the sequence and structure of the 27-mer RNA targetcorresponding to the 16S rRNA A-site.

FIG. 2 shows the ESI-CID-MS of a 27-mer RNA/DNA hybrid in the presenceand absence of paromomycin.

FIG. 3 shows the ESI-MS of a 27-mer RNA/DNA hybrid target in thepresence of paromomycin alone (panel a), and in the presence of bothparomomycin and a combinatorial library (panel b).

FIG. 4 shows the ESI-CID-MS spectrum of a combinatorial librarymember-27mer RNA/DNA hybrid noncovalent complex ion of m/z 1919.0.

FIG. 5 shows the ESI-MS of a combinatorial library screened against a27mer RNA/DNA hybrid.

FIG. 6 shows the ESI-MS-MS analysis of the signal of m/z 1917.8 uarising from the binding of a member of mass 665 from anothercombinatorial library.

FIG. 7 shows the ESI-MS-MS analysis of the signal of m/z 1934.3 uarising from the binding of a member of mass 720 from a library.

FIGS. 8 and 9 show graphical representations of the abundances of w anda-Base ions resulting from (CID) of ions from a DNA:DNA duplex.

FIGS. 10, 11 and 12 depict MASS analyses to determine the binding ofligands to a molecular interaction site.

FIG. 13 depicts high precision ESI-FTICR mass measurement of theinteraction of the 16S A site of an RNA complexed with paromomycin.

FIG. 14 depicts FTMS spectrum obtained from a mixture of a 16S RNA model(10 μM) and a 60-member combinatorial library.

FIG. 15 depicts an expanded view of the 1863 complex from FIG. 15.

FIG. 16 depicts mass of a binding ligand determined from a startinglibrary-of compounds.

FIG. 17 depicts high resolution ESI-FTICR spectrum of the library usedin FIGS. 15 and 16.

FIG. 18 depicts use of exact mass measurements and elemental constraintsto determine the elemental composition of an exemplary “unknown” bindingligand.

FIG. 19 depicts ESI-MS measurements of a solution containing a fixedconcentration of RNA at different concentrations of ligand.

FIG. 20 depicts a preferred schematic representation for thedetermination of ligand binding site by tandem mass spectrometry.

FIG. 21 depicts MASS screening of a 27 member library against a 27-merRNA construct representing the prokaryotic 16S A-site.

FIG. 22 depicts MS/MS of a 27-mer RNA construct representing theprokaryotic 16S A-site containing deoxyadenosine residues at theparomomycin binding site.

FIG. 23 depicts MS-MS spectra obtained from a mixture of a 27-mer RNAconstruct representing the prokaryotic 16S A-site containingdeoxyadenosine residues at the paromomycin binding and the 216 membercombinatorial library.

FIG. 24 depicts secondary structures of the 27 base RNA models used inthis work corresponding to the 18S (eukaryotic) and 16S (prokaryotic)A-sites.

FIG. 25 depicts ESI-FTICR spectrum of a mixture of 27-baserepresentations of the 16S A-site with (7 μM) and without (1 μM) an 18atom neutral mass tag attached to the 5-terminus in the presence of 500nM paromomycin.

FIG. 26 depicts mass spectra from simultaneous screening of 16S A-siteand 18S A-site Model RNAs against a mixture of aminoglycosides.

FIG. 27 depicts sequences and structures for oligonucleotides R and C.

FIG. 28A depicts mass spectrum obtained from a mixture of 5 μM C and 125nM paromomycin.

FIG. 28B depicts MS-MS spectrum obtained following isolation of [M-5H]⁵⁻ions (m/z 1783.6) from uncomplexed C.

FIG. 28C depicts MS-MS spectrum obtained following isolation of [M-5H]⁵⁻ions (m/z 1907.5) from C complexed with paromomycin.

FIG. 29A depicts MS-MS spectrum obtained from a mixture of 10 μM C and a216 member combinatorial library following isolation of [M-5H]⁵⁻ ions(m/z 1919.0) from C complexed with ligands of mass 676.0±0.6.

FIG. 29B depicts MS-MS spectrum obtained from a mixture of 10 μM C and a216 member combinatorial library following isolation of [M-5H]⁵⁻ ions(m/z 1934.3) from C complexed with ligands of mass 753.5±0.6.

FIG. 30 depicts electrospray ionization Fourier transform ion cyclotronresonance mass spectrometry of a target/putative ligand mixture.

FIG. 31 shows isotope clusters from the spectrum of FIG. 30.

FIG. 32 depicts data tabulated and stored in a relational database.

FIG. 33 shows an exemplary flow chart for a computer program foreffecting certain methods in accordance with the invention.

SUMMARY OF EXEMPLARY MASS SPECTROMETRIC TECHNIQUES

Mass spectrometry (MS) is a powerful analytical tool for the study ofmolecular structure and interaction between small and large molecules.The current state-of-the-art in MS is such that less than femtomolequantities of material can be readily analyzed using mass spectrometryto afford information about the molecular contents of the sample. Anaccurate assessment of the molecular weight of the material may bequickly obtained, irrespective of whether the sample's molecular weightis several hundred, or in excess of a hundred thousand, atomic massunits or Daltons (Da). It has now been found that mass spectrometry canelucidate significant aspects of important biological molecules. Onereason for the utility of MS as an analytical tool in accordance withthe invention is the availability of a variety of different MS methods,instruments, and techniques which can provide different pieces ofinformation about the samples.

One such MS technique is electrospray ionization mass spectrometry(ESI-MS) (Smith et al., Anal. Chem., 1990, 62, 882-899; Snyder, inBiochemical and biotechnological applications of electrospray ionizationmass, American Chemical Society, Washington, D.C., 1996; Cole, inElectrospray ionization mass spectrometry: fundamentals,instrumentation, Wiley, N.Y., 1997). ESI produces highly chargeddroplets of the sample being studied by gently nebulizing the samplesolution in the presence of a very strong electrostatic field. Thisresults in the generation of highly charged droplets that shrink due toevaporation of the neutral solvent and ultimately lead to a “Coulombicexplosion” that affords multiply charged ions of the sample material,typically via proton addition or abstraction, under mild conditions.ESI-MS is particularly useful for very high molecular weight biopolymerssuch as proteins and nucleic acids greater than 10 kDa in mass, for itaffords a distribution of multiply-charged molecules of the samplebiopolymer without causing any significant amount of fragmentation. Thefact that several peaks are observed from one sample, due to theformation of ions with different charges, contributes to the accuracy ofESI-MS when determining the molecular weight of the biopolymer becauseeach observed peak provides an independent means for calculation of themolecular weight of the sample. Averaging the multiple readings ofmolecular weight so obtained from a single ESI-mass spectrum affords anestimate of molecular weight that is much more precise than would beobtained if a single molecular ion peak were to be provided by the massspectrometer. Further adding to the flexibility of ESI-MS is thecapability to obtain measurements in either the positive or negativeionization modes.

In recent years electrospray ionization mass spectrometry (ESI-MS) hasgrown extensively as an analytical technique due to its broadapplicability for analysis of macromolecules, including proteins,nucleic acids, and carbohydrates. Bowers, et al., Journal of PhysicalChemistry, 1996, 100, 12897-12910; Burlingame, et al., J. Anal. Chem.,1998, 70, 647R-716R; Biemann, Ann. Rev. Biochem., 1992, 61, 977-1010;and Crain, et al., Curr. Opin. Biotechnol., 1998, 9, 25-34. One of themost significant developments in the field has been the observation,under appropriate solution conditions and analyte concentrations, ofspecific non-covalently associated macromolecular complexes that havebeen promoted into the gas-phase intact. Loo, Mass Spectrometry Reviews,1997, 16, 1-23; Smith, et al., Chemical Society Reviews, 1997, 26,191-202; Ens, et al., Standing, K. G. and Chemushevich, I. V. Editors,New Methods for the Study of Biomolecular Complexes (Proceedings of theNATO Advanced Research Workshop, held Jun. 16-20, 1996, in Alberta,Canada In: NATO ASI Ser., Ser. C, 1998; 510; Kluwer, Dordrecht, Neth.,1998. Recent examples include multimeric proteins (Fitzgerald, et al.,Proc. Nat'l. Acad. Sci. USA, 1996, 93, 6851-6856), enzyme-ligandcomplexes (Ganguly, et al., Tetrahedron, 1993, 49, 7985-7996),protein-DNA complexes (Cheng, et al., Proc. Nat'l. Acad. Sci. U.S.A.,1996, 93, 7022-7027), multimeric DNA complexes (Griffey, et al., Proc.SPIE-Int. Soc. Opt. Eng., 1997, 2985, 82-86), and DNA-drug complexes(Gale, et al., JACS, 1994, 116, 6027-6028), the disclosures of which areincorporated herein by reference in their entirety.

Smith and co-workers have demonstrated that under competitive bindingconditions in solution, ESI-MS measurements of enzyme-ligand mixturesyield gas-phase ion abundances that correlate with measuredsolution-phase dissociation constants (K_(D)). Cheng, et al., JACS,1995, 117, 8859-8860, the disclosure of which is incorporated herein byreference in its entirety. They were able to rank the binding affinitiesof a 256-member library of modified benzenesulfonamide inhibitors tocarbonic anhydrase. Levels of free and bound ligands and substrates canbe quantified directly from their relative abundances as measured byESI-MS and that these measurements can be used to quantitativelydetermine molecular dissociation constants that agree with solutionmeasurements. Jorgensen and co-workers have demonstrated that therelative ion abundance of non-covalent complexes formed between D- andL-tripeptides and vancomycin group antibiotics can be used to measuresolution binding constants. Jorgensen, et al., Anal. Chem., 1998, 70,4427-4432, the disclosure of which is incorporated herein by referencein its entirety. Griffey and co-workers have shown that tandem ESI-MSmethods can be used to determine the binding sites for small moleculesthat bind to RNA targets. Gale, et al., Journal of the American Societyfor Mass Spectrometry, 1995, 6, 1154-1164, the disclosure of which isincorporated herein by reference in its entirety.

Fourier transform ion cyclotron resonance mass spectrometry (FT-ICR MS)can resolve very small mass differences providing determination ofmolecular mass with unparalleled precision and accuracy. Marshall, etal., Mass Spectrom. Rev., 1998, 17, 1-35. Because each small moleculewith a unique elemental composition carries an intrinsic mass labelcorresponding to its exact molecular mass, identifying closely relatedlibrary members bound to a macromolecular target requires only ameasurement of exact molecular mass. The target and potential ligands donot require radiolabeling, fluorescent tagging, or deconvolution viasingle compound re-synthesis. Furthermore, adjustment of theconcentration of ligand and target allows ESI-MS assays to be run in aparallel format under competitive or non-competitive binding conditions.Signals can be detected from complexes with dissociation constantsranging from <10 nM to ˜100 mM.

Small molecules that bind to structured regions of RNA can exhibittherapeutic effects. For example, aminoglycoside antibiotics inhibitbacterial growth by disrupting essential RNA-protein and RNA-RNAinteractions. De Stasio, et al, EEMBO J, 1989, 8, 1213-6 and Bryan, L.E. In New dimensions in antimicrobial therapy; Root, R. K., Sande, M.A., Eds., Churchill Livingstone, New York, 1984; Vol. 1, pp 17-35.Paromomycin, one of the most widely studied aminoglycosides, binds tothe decoding region of the prokaryotic 16S rRNA (the A-site) with a ˜200nM KD and induces misreading of the genetic code during translation.Wong, et al., Chem. Biol., 1998, 5, 397-406. However, the features ofthe interaction between RNAs and aminoglycosides that provide bindingspecificity are poorly characterized. In this work we employ ESI-FTICRto detect specific interactions between two closely related model RNAconstructs corresponding to the decoding sites of the prokaryotic andeukaryotic ribosomes and individual members of a collection ofaminoglycoside antibiotics.

Matrix-Assisted Laser Desorption/Ionization Mass Spectrometry (MALDI-MS)is another method that can be used for studying biomolecules (Hillenkampet al., Anal. Chem., 1991, 63, 1193A-1203A). This technique ionizes highmolecular weight biopolymers with minimal concomitant fragmentation ofthe sample material. This is typically accomplished via theincorporation of the sample to be analyzed into a matrix that absorbsradiation from an incident UV or IR laser. This energy is thentransferred from the matrix to the sample resulting in desorption of thesample into the gas phase with subsequent ionization and minimalfragmentation. One of the advantages of MALDI-MS over ESI-MS is thesimplicity of the spectra obtained as MALDI spectra are generallydominated by singly charged species. Typically, the detection of thegaseous ions generated by MALDI techniques, are detected and analyzed bydetermining the time-of-flight (TO) of these ions. While MALDI-TOF MS isnot a high resolution technique, resolution can be improved by makingmodifications to such systems, by the use of tandem MS techniques, or bythe use of other types of analyzers, such as Fourier transform (FT) andquadrupole ion traps.

Fourier transform mass spectrometry (FTMS) is an especially usefulanalytical technique because of its ability to make mass measurementswith a combination of accuracy and resolution that is superior to otherMS detection techniques, in connection with ESI or MALDI ionization(Amster, J. Mass Spectrom., 1996, 31, 1325-1337). Further it may be usedto obtain high resolution mass spectra of ions generated by any of theother ionization techniques. The basis for FTMS is ion cyclotron motion,which is the result of the interaction of an ion with a unidirectionalmagnetic field. The mass-to-charge ratio of an ion (m/q or m/z) isdetermined by a FTMS instrument by measuring the cyclotron frequency ofthe ion. The insensitivity of the cyclotron frequency to the kineticenergy of an ion is one of the fundamental reasons for the very highresolution achievable with FTMS. FTMS is an excellent detector inconventional or tandem mass spectrometry, for the analysis of ionsgenerated by a variety of different ionization methods including ESI andMALDI, or product ions resulting from collisionally activateddissociation (CAD).

Collisionally activated dissociation (CAD), also known as collisioninduced dissociation (CID), is a method by which analyte ions aredissociated by energetic collisions with neutral or charged species,resulting in fragment ions which can be subsequently mass analyzed. Massanalysis of fragment ions from a selected parent ion can provide certainsequence or other structural information relating to the parent ion.Such methods are generally referred to as tandem mass spectrometry (MSor MS/MS) methods and are the basis of the some of MS based biomolecularsequencing schemes being employed today.

FTICR-MS, like ion trap and quadrupole mass analyzers, allows selectionof an ion that may actually be a weak non-covalent complex of a largebiomolecule with another molecule (Marshall and Grosshans, Anal. Chem.,1991, 63, A215-A229; Beu et al., J. Am. Soc. Mass Spectrom., 1993, 4,566-577; Winger et al., J. Am. Soc. Mass Spectrom., 1993, 4, 566-577);(Huang and Henion, Anal. Chem., 1991, 63, 732-739), or hyphenatedtechniques such as LC-MS (Bruins, Covey and Henion, Anal. Chem., 1987,59, 2642-2646 Huang and Henion, J. Am. Soc. Mass Spectrom., 1990, 1,158-65; Huang and Henion, Anal. Chem., 1991, 63, 732-739) and CE-MS (Caiand Henion, J. Chromatogr., 1995, 703, 667-692) experiments. FTICR-MShas also been applied to the study of ion-molecule reaction pathways andkinetics.

So-called “Hyphenated” techniques can be used for structure elucidationbecause they provide the dual features of separation and mass detection.Such techniques have been used for the separation and identification ofcertain components of mixtures of compounds such as those isolated fromnatural products, synthetic reactions, or combinatorial chemistry.Hyphenated techniques typically use a separation method as the firststep; liquid chromatography methods such as HPLC, microbore LC,microcapillary LC, or capillary electrophoresis are typical separationmethods used to separate the components of such mixtures. Many of theseseparation methods are rapid and offer high resolution of componentswhile also operating at low flow rates that are compatible with MSdetection. In those cases where flow rates are higher, the use of‘megaflow’ ESI sources and sample splitting techniques have facilitatedtheir implementation with on-line mass spectrometry. The second stage ofthese hyphenated analytical techniques involves the injection ofseparated components directly into a mass spectrometer, so that thespectrometer serves as a detector that provides information about themass and composition of the materials separated in the first stage.While these techniques are valuable from the standpoint of gaining anunderstanding of the masses of the various components of multicomponentsamples, they are incapable of providing structural detail. Somestructural detail, however, may be ascertained through the use of tandemmass spectrometry, e.g., hydrogen/deuterium exchange or collisioninduced disassociation.

Typically, tandem mass spectrometry (MS^(n)) involves the coupled use oftwo or more stages of mass analysis where both the separation anddetection steps are based on mass spectrometry. The first stage is usedto select an ion or component of a sample from which further structuralinformation is to be obtained. This selected ion is then fragmented by(CID) or photodissociation. The second stage of mass analysis is thenused to detect and measure the mass of the resulting fragments orproduct ions. The advent of FTICR-MS has made a significant impact onthe utility of tandem, MS^(n) procedures because of the ability of FTICRto select and trap specific ions of interest and its high resolution andsensitivity when detecting fragment ions. Such ion selection followed byfragmentation routines can be performed multiple times so as toessentially completely dissect the molecular structure of a sample. Atwo-stage tandem MS experiment would be called a MS-MS experiment whilean n-stage tandem MS experiment would be referred to as a MS^(n)experiment. Depending on the complexity of the sample and the level ofstructural detail desired, MS^(n) experiments at values of n greaterthan 2 may be performed.

Ion trap-based mass spectrometers are particularly well suited for suchtandem experiments because the dissociation and measurement steps aretemporarily rather than spatially separated. For example, a commonplatform on which tandem mass spectrometry is performed is a triplequadrupole mass spectrometer. The first and third quadrupoles serve asmass filters while the second quadrupole serves as a collision cell forCAD. In a trap based mass spectrometer, parent ion selection anddissociation take place in the same part of the vacuum chamber and areeffected by control of the radio frequency wavelengths applied to thetrapping elements and the collision gas pressure. Hence, while a triplequadrupole mass analyzer is limited to two stages of mass spectrometry(i.e. MS/MS), ion trap-based mass spectrometers can perform MS^(n)analysis in which the parent ion is isolated, dissociated, mass analyzedand a fragment ion of interest is isolated, further dissociated, andmass analyzed and so on. A number of MS⁴ procedures and higher haveappeared in the literature in recent years and can be used here. (Chenget al., Techniques in Protein Chemistry, VII, pp. 13-21).

ESI and MALDI techniques have found application for the rapid andstraightforward determination of the molecular weight of certainbiomolecules (Feng and Konishi, Anal. Chem., 1992, 64, 2090-2095;Nelson, Dogruel and Williams, Rapid Commun. Mass Spectrom., 1994, 8,627-631). These techniques have been used to confirm the identity andintegrity of certain biomolecules such as peptides, proteins,oligonucleotides, nucleic acids, glycoproteins, oligosaccharides andcarbohydrates. Further, these MS techniques have found biochemicalapplications in the detection and identification of post-translationalmodifications on proteins. Verification of DNA and RNA sequences thatare less than 100 bases in length has also been accomplished using ESIwith FTMS to measure the molecular weight of the nucleic acids (Littleet al, Proc. Natl. Acad. Sci. USA, 1995, 92, 2318-2322).

ESI tandem MS has been used for the study of high molecular weightproteins, for peptide and protein sequencing, identification ofpost-translational modifications such as phosphorylation, sulfation orglycosylation, and for the study of enzyme mechanisms (Rossomando etal., Proc. Natl. Acad. Sci. USA, 1992, 89, 5779-578; Knight et al.,Biochemistry, 1993, 32, 2031-2035). Covalent enzyme-intermediate orenzyme-inhibitor complexes have been detected using ESI and analyzed byESI-MS to ascertain the site(s) of modification on the enzyme. Theliterature has shown examples of protein sequencing where the multiplycharged ions of the intact protein are subjected to collisionallyactivated dissociation to afford sequence informative fragment ions(Light-Wahl et al., Biol. Mass Spectrom., 1993, 22, 112-120). ESI tandemMS has also been applied to the study of oligonucleotides and nucleicacids (Ni et al., Anal. Chem., 1996, 68, 1989-1999; Little, Thannhauserand McLafferty, Proc. Natl. Acad. Sci., 1995, 92, 2318-2322).

While tandem ESI mass spectra of oligonucleotides are often complex,several groups have successfully applied ESI tandem MS to the sequencingof large oligonucleotides (McLuckey, Van Berkel and Glish, J. Am. Soc.Mass Spectrom., 1992, 3, 60-70; McLuckey and Habibigoudarzi, J. Am.Chem. Soc., 1993, 115, 12085-12095; Little et al., J. Am. Chem. Soc.,1994, 116, 4893-4897). General rules for the principal dissociationpathways of oligonucleotides, as formulated by McLuckey (McLuckey, VanBerkel and Glish, J. Am. Soc. Mass Spectrom., 1992, 3, 60-70; McLuckeyand Habibigoudarzi, J. Am. Chem. Soc., 1993, 115, 12085-12095), haveassisted interpretation of mass spectra of oligonucleotides, and includeobservations of fragmentation such as, for example, the stepwise loss ofbase followed by cleavage of the 3′—C—O bond of the relevant sugar.Besides the use of ESI with tandem MS for oligonucleotide sequencing,two other mass spectrometric methods are also available: mass analysisof products of enzymatic cleavage of oligonucleotides (Pieles et al.,Nucleic Acids Res., 1993, 21, 3191-3196; Shaler et al., Rapid Commun.Mass Spectrom., 1995, 9, 942-947; Glover et al., Rapid Commun. MassSpectrom., 1995, 9, 897-901), and the mass analysis of fragment ionsarising from the initial ionization/desorption event, without the use ofmass selection techniques (Little et al., Anal. Chem., 1994, 66,2809-2815; Nordhoff et al., J. Mass Spectrom., 1995, 30, 99-112; Littleet al., J. Am. Chem. Soc., 1994, 116, 4893-4897; Little and McLafferty,J. Am. Chem. Soc., 1995, 117, 6783-6784). While determining the sequenceof deoxyribonucleic acids (DNA) is possible using ESI-MS and CIDtechniques (McLuckey, Van Berkel and Glish, J. Am. Soc. Mass Spectrom.,1992, 3, 60-70; McLuckey and Habibigoudarzi, J. Am. Chem. Soc., 1993,115, 12085-12095), the determination of RNA sequence is much moredifficult. Thus while small RNA, such as 6-mers, have been sequenced(McCloskey et al., J. Am. Chem. Soc., 1993, 115, 12085-1095), larger RNAhave been difficult to sequence using mass spectrometry.

Electrospray mass spectrometry has been used to study biochemicalinteractions of biopolymers such as enzymes, proteins and nucleic acidswith their ligands, receptors, substrates or inhibitors. Whileinteractions that lead to covalent modification of the biopolymer havebeen studied for some time, those interactions that are of anon-covalent nature have been particularly difficult to study heretoforeby methods other than kinetic techniques. It is now possible to yieldinformation on the stoichiometry and nature of such non-covalentinteractions from mass spectrometry. MS can provide information aboutthe interactions between biopolymers and other molecules in the gasphase; however, experiments have demonstrated that the data so generatedcan be reflective of the solution phase phenomena from which the massspectra were generated.

ESI is a gentle ionization method that results in no significantmolecular fragmentation and preserves even weakly bound complexesbetween biopolymers and other molecules so that they are detected intactwith mass spectrometry. A variety of non-covalent complexes ofbiomolecules have been studied using ESI-MS and reported in theliterature (Loo, Bioconjugate Chemistry, 1995, 6, 644-665; Smith et al.,J. Biol. Mass Spectrom. 1993, 22, 493-501; Li et al., J. Am. Chem. Soc.,1993, 115, 8409-8413). These include the peptide-protein complexes(Busman et al., Rapid Commun. Mass Spectrom., 1994, 8, 211-216; Loo,Holsworth and Root-Bernstein, Biol. Mass Spectrom., 1994, 23, 6-12;Anderegg and Wagner, J. Am. Chem. Soc., 1995, 117, 1374-1377;Baczynskyj, Bronson and Kubiak., Rapid Commun. Mass Spectrom., 1994, 8,280-286), interactions of polypeptides and metals (Loo, Hu and Smith, J.Am. Soc. Mass Spectrom., 1994, 5, 959-965; Hu and Loo, J. MassSpectrom., 1995, 30, 1076-1079; Witkowska et al., J. Am. Chem. Soc.,1995, 117, 3319-3324; Lane et al., J. Cell Biol., 1994, 125, 929-943),protein-small molecule complexes (Ganem and Henion, ChemTracts-Org.Chem., 1993, 6, 1-22; Henion et al., Ther. Drug Monit., 1993, 15,563-569; Baca and Kent, J. Am. Chem. Soc., 1992, 114, 3992-3993), thestudy of the quaternary structure of multimeric proteins (Baca and Kent,J. Am. Chem. Soc., 1992, 114., 3992-3993; Light-Wahl, Schwartz andSmith, J. Am. Chem. Soc., 1994, 116, 5271-5278; Loo, J. Mass Spectrom.,1995, 30, 180-183), and the study of nucleic acid complexes (Light-Wahlet al., J. Am. Chem. Soc., 1993, 115, 803-804; Gale et al., J. Am. Chem.Soc., 1994, 116, 6027-6028; Goodlett et al., Biol. Mass Spectrom., 1993,22, 181-183; Ganem, Li and Henion, Tet. Lett., 1993, 34, 1445-1448;Doctycz et al., Anal. Chem., 1994, 66, 3416-3422; Bayer et al., Anal.Chem., 1994, 66, 3858-3863; Greig et al., J. Am. Chem. Soc., 1995, 117,10765-766).

While data generated and conclusions reached from ESI-MS studies forweak non-covalent interactions generally reflect, to some extent, thenature of the interaction found in the solution-phase, it has beenpointed out in the literature that control experiments are necessary torule out the possibility of ubiquitous non-specific interactions (Smithand Light-Wahl, Biol. Mass Spectrom., 1993, 22, 493-501). Some haveapplied the use of ESI-MS and MALDI-MS to the study of multimericproteins for the gentleness of the electrospray/desorption processallows weakly bound complexes, held together by hydrogen bonding,hydrophobic and/or ionic interactions, to remain intact upon transfer tothe gas phase. The literature shows that not only do ESI-MS data fromgas-phase studies reflect the non-covalent interactions found insolution, but that the strength of such interactions may also bedetermined. The binding constants for the interaction of various peptideinhibitors to src SH2 domain protein, as determined by ESI-MS, werefound to be consistent with their measured solution phase bindingconstants (Loo, Hu and Thanabal, Proc. 43^(rd) ASMS Conf. on MassSpectrom. and Allied Topics, 1995). ESI-MS has also been used togenerate Scatchard plots for measuring the binding constants ofvancomycin antibiotics with tripeptide ligands (Lim et al., J. MassSpectrom., 1995, 30, 708-714).

Similar experiments have been performed to study non-covalentinteractions of nucleic acids. Both ESI-MS and MALDI-MS have beenapplied to study the non-covalent interactions of nucleic acids andproteins. While MALDI does not typically allow for survival of an intactnon-covalent complex, the use of crosslinking methods to generatecovalent bonds between the components of the complex allows for its usein such studies. Stoichiometry of interaction and the sites ofinteraction have been ascertained for nucleic acid-protein interactions(Jensen et al., Rapid Commun. Mass Spectrom., 1993, 7, 496-501; Jensenet al., 42^(nd) ASMS Conf. on Mass Spectrom. and Allied Topics, 1994,923). The sites of interaction are typically determined by proteolysisof either the non-covalent or covalently crosslinked complex (Jensen etal., Rapid Commun. Mass Spectrom., 1993, 7, 496-501; Jensen et al.,42^(nd) ASMS Conf. on Mass Spectrom. and Allied Topics, 1994, 923; Cohenet al., Protein Sci., 1995, 4, 1088-1099). Comparison of the massspectra with those generated from proteolysis of the protein aloneprovides information about cleavage site accessibility or protection inthe nucleic acid-protein complex and, therefore, information about theportions of these biopolymers that interact in the complex.

Electrospray mass spectrometry has also been effectively used for thedetermination of binding constants of noncovalent macromolecularcomplexes such as those between proteins and ligands, enzymes andinhibitors, and proteins and nucleic acids. Greig et al. (J. Am. Chem.Soc., 1995, 117, 10765-10766) have reported the use of ESI-MS todetermine the dissociation constants (K_(D)) for oligonucleotide-bovineserum albumin (BSA) complexes. The K_(D) values determined by ESI-MSwere reported to match solution KD values obtained using capillaryelectrophoresis.

Cheng et al. (J. Am. Chem. Soc., 1995, 117, 8859-8860) have reported theuse of ESI-FTICR mass spectrometry as a method to determine thestructure and relative binding constants for a mixture of competitiveinhibitors of the enzyme carbonic anhydrase. Using a single ESI-FTICR-MSexperiment these researchers were able to ascertain the relative bindingconstants for the noncovalent interactions between inhibitors and theenzyme by measuring the relative abundances of the ions of thesenoncovalent complexes. Further, the K_(D)s so determined for thesecompounds paralleled their known binding constants in solution. Themethod was also capable of identifying the structures of tight bindingligands from small mixtures of inhibitors based on the high resolutioncapabilities and multistep dissociation mass spectrometry afforded bythe FTICR technique. In a related study, Gao et al. (J. Med. Chem.,1996, 39, 1949-55) have reported the use of ESI-FTICR-MS to screenlibraries of soluble peptides in a search for tight binding inhibitorsof carbonic anhydrase II. Simultaneous identification of the structureof a tight binding peptide inhibitor and determination of its bindingconstant was performed. The binding affinities determined from massspectral ion abundance were found to correlate well with thosedetermined in solution experiments. Further, the applicability of thistechnique to drug discovery efforts is limited by the lack ofinformation generated with regards to sites and mode of such noncovalentinteractions between a protein and ligands.

Also, these methods discuss, and appear to be limited to, the study ofligand interactions with proteins. The suitability of this method ofmass spectrometric analysis of binding and dissociation constants forthe study of noncovalent interactions of oligonucleotides, nucleicacids, such as RNA and DNA, and other biopolymers has not been describedin the literature.

The drug discovery process has recently been revolutionized by theintroduction of high throughput synthesis and combinatorial chemistrywhich afford collections and mixtures of large numbers of syntheticcompounds for the purpose of screening for biological activity. Suchlarge mixtures and pools of compounds pose significant challenges forthe bioassay and analytical scientist. The analytical challenge istwo-fold: separation of the active component of a mixture, and theidentification of its structure. A variety of separation methods areavailable, including LC, HPLC, and CE. However, from the standpoint ofseparating biologically active components from a mixture of one or moretargets with a combinatorial library necessitates the use anddevelopment of methods that select for and separate the complex (usuallynoncovalent) between the ligands and the target. Affinity column methodshave been used to selectively isolate and subsequently analyze bindingcomponents of mixtures of compounds. For example, Kassel et al. (Kasselet al., Techniques in Protein Chemistry VI, J. Crabb, Ed., AcademicPress, San Diego, 1995, 39-46) have used an immobilized src SH2 domainprotein column to separate and then analyze by HPLC-ESI-MS the structureof high affinity binding phosphopeptides.

A similar technique, ACE-ESI-MS, uses affinity capillary electrophoresisto accomplish the separation of noncovalent complexes formed upon mixinga biomolecular target with a combinatorial library or mixture ofcompounds. The receptor is typically incorporated into the capillary sothat those ligands present in the combinatorial mixture interact withthe target and are retained or slowed down within the capillary. Onceseparated, these noncovalent complexes are analyzed on-line by ESI-MS toascertain the structures of the complexes and bound components. Thismethod incorporates into one, the two steps that were previouslyperformed separately: the compound/noncovalent complex selection, as haspreviously been demonstrated for vancomycin (Chu et al., Acc. Chem.Res., 1995, 28, 461-468; Chu et al., J. Org. Chem., 1993, 58, 648-52)and the step of compound identification (Cai and Henion, J. Chromatogr.,1995, 703, 667-692). For example, ACE-ESI-MS has been applied tomixtures of vancomycin with peptide libraries (Chu et al., J. Am. Chem.Soc., 1996, 118, 7827-35) to allow rapid screening of noncovalentcomplexes formed, and the identification of peptides that bind tovancomycin.

Another method for the separation and identification of activecomponents from combinatorial libraries is the use of size-exclusionchromatography (SEC) followed by LC/MS or CE/MS analysis. Size exclusionis a simple yet powerful method to separate a biopolymer target and itscomplexes with small molecules members of a combinatorial library. Onceisolated by SEC, these complexes are dissociated, under denaturingsolution conditions, and finally the binding ligands are analyzed bymass spectrometry. This method has been applied to the identification ofhigh affinity ligands for human serum albumin (HSA) from combinatoriallibrary of small molecules (Dunayevskiy et al., Rapid Commun. MassSpectrom., 1997, 11, 1178-84).

Bio-affinity characterization mass spectrometry (BACMS) is yet anothermethod for the characterization of noncovalent interactions of mixturesof ligands and biomolecular targets (Bruce et al., Rapid Commun. MassSpectrom., 1995, 9, 644-50). BACMS involves the electrospray ionizationof a solution containing both the affinity target and a mixture ofligands (or a combinatorial library), followed by trapping of all theionic species in the FTICR ion-trap. The complexes of interest are thenidentified in the mass spectrum and isolated by selected-ionaccumulation. This is followed by low energy dissociation or ‘heating’to separate the high binding affinity ligands present in the complex.Finally, collisionally activated dissociation (CAD) is used to providestructural information about the high binding affinity ligand. Thegreatest advantage of BACMS is that the time-consuming techniquesusually needed for the study of libraries, such as affinitychromatography, using solid supports for separation and purification ofthe complexes, followed by analysis to characterize the selectedligands, are all combined into one FTICR-MS experiment. To date, BACMShas only been applied to the study of protein targets.

None of the foregoing methods, however, have demonstrated applicabilityto a variety of biomolecular targets. Further, such methods do notprovide rapid determination of the site of interaction between acombinatorially derived ligand and biopolymer.

Tandem mass spectrometry, as performed using electrospray ionization(ESI) on FTICR, triple quadrupole, or ion-trap mass spectrometers, hasbeen found to be a powerful tool for determining the structure ofbiomolecules. It is known in the art that both small and large (>3000kbase) RNA and DNA may be transferred from solution into the gas phaseas intact ions using electrospray techniques. Further it is known, tothose skilled in the art that these ions retain some degree of theirsolution structures as ions in the gas phase; this is especially usefulwhen studying noncovalent complexes of nucleic acids and proteins, andnucleic acids and small molecules by mass spectrometric techniques.

SUMMARY OF CERTAIN PREFERRED EMBODIMENTS

Studies have demonstrated that oligonucleotides and nucleic acids obeycertain fragmentation patterns during collisionally induced dissociation(CID), and that these fragments and patterns can be used to determinethe sequence of the nucleic McLuckey, Van Berkel and Glish, J. Am. Soc.Mass Spectrom., 1992, 3, 60-70; McLuckey and Habibigoudarzi, J. Am.Chem. Soc., 1993, 115, 12085-12095). Electrospray ionization producesseveral multiply charged ions of the parent nucleic acid, without anysignificant fragmentation of the nucleic acid. Typically, a singlecharge state of the nucleic acid is isolated using a triple quadrupoleion trap, or ion cyclotron resonance (ICR) device. This ion is thenexcited and allowed to collide with a neutral gas such as helium, argonor nitrogen so as to afford cleavage of certain bonds in the nucleicacid ion, or excited and fragmented with a laser pulse. Typically, twoseries of fragment ions are found to be formed: the a-Base series, andthe w-series.

The series of a-Base fragments originates from initial cleavage of theglycosidic bond by simultaneous abstraction of a C-2′ proton, followedby the elimination of the 3′-phosphategroup and the C-4′ proton. Thisfragmentation scheme results in a residual furan attached to the3′-phosphate and affords a series of a-Base fragments whose massesincrease sequentially from the 5′-terminus of the nucleic acid.Measurement of the masses of these collisionally induced fragmentstherefore affords the determination of the sequence of the nucleic acidin the 5′ to 3′ direction. The w series of fragments is generated viacleavage of the nucleic acid in a manner that leaves a 5′phosphateresidue on each fragment. Thus monitoring the masses of w-seriesfragments allows determination of the sequence of the nucleic acid inthe 3′ to 5′ direction. Using the sequence information generated fromboth series of fragments the sequence of deoxyribonucleic acids (DNA)may be ascertained. Obtaining similar mass spectrometric information forribonucleic acids (RNA), is a much more difficult task. Collisionallyinduced dissociation (CID) of RNA is much less energetically favoredthan is the case for DNA because of the greater strength of theglycosidic bond in RNA. Hence, while small RNA such as 6-mers have beensequenced using CID MS, the sequencing of larger RNA has not beengenerally successful using tandem MS.

Determination of the structure of biomolecules, such as proteins andnucleic acids, may be attempted using solution biochemical cleavagefollowed by mass spectrometry. However, these methods are cumbersome andnot always successful in that several biochemical cleavage andseparation steps need to be performed prior to MS analysis of thecleaved products. Also, the level of information provided with regardsto secondary and tertiary structure of biomolecules is limited. Methodsavailable in the scientific literature are therefore greatly limited interms of the sequence and structural information they provide forbiomolecules and biomolecular targets.

One aspect of the present invention provides methods for determining thestructure of biomolecular targets such as nucleic acids using massspectrometry. The structure of nucleic acids, especially RNA, which isoften difficult to ascertain, is readily determined using the methods ofthis invention. The structure of a nucleic acid is determined from thefragmentation pattern observed in MS^(n) experiments. Directedfragmentation of RNA is facilitated by the selective incorporation ofdeoxynucleotides or other nucleosidic residues at specific residuelocations in the nucleic acid sequence. During CID of such RNA/DNAchimeric nucleic acids, cleavage is facilitated at the sites wheredeoxynucleotides or the other non-native residues were incorporated.Cleavage is also influenced by the local secondary and tertiarystructure of the biomolecule. Therefore, the cleavage patterns observedfrom a RNA/DNA hybrid reveals the local structure of the nucleic acid,including mismatched base pairs, bulged regions and other features.

Since exposed deoxynucleotide residues are known to be susceptible toCID cleavage in MS experiments, the systematic incorporation of suchresidues into RNA allows the systematic exploration of the localstructure of RNA. Using this embodiment of the invention, it is possibleto determine the secondary and tertiary structure of nucleic acids,including features such as mismatched base pairs, loops, bulges, andkink and stem structures.

Determination of the structure of an RNA may be accomplished, usingexemplary methods of the invention, as follows. An RNA whose structureis to be determined is synthesized using an automated nucleic acidsynthesizer. During RNA synthesis, deoxynucleotides are selectivelyincorporated into the sequence at specific sites where the structure isto be probed. This RNA/DNA chimeric nucleic acid, which is sensitized tocollisional activation, is now used for sequence and structuredetermination using tandem MS experiments. ESI-MS, followed by trappingof selected ions and subsequent CID of each ion, affords information asto which positions of the nucleic acid hybrid are disordered (or notparticipating in a higher order structure) and, therefore, available forcleavage. A systematic pattern of deoxynucleotide incorporation into thesequence of the test RNA allows a systematic, mass spectrometricassessment of structure in a certain area of the nucleic acid, or forthe entire nucleic acid. Other modified nucleic acid residues may beused instead of DNA. This, chemically modified nucleic acid subunitssuch as Z¹-modified, e.g. 2¹-O-Alkyl, base-modified, backbone modifiedor other residues may serve. Such residues will permit assessment of DNAas well as RNA.

The present invention also provides methods for the determination of thesite and nature of interactions between a biomolecular target and abinding ligand. This is information of critical value to the process ofdrug discovery. Current methods of biomolecular screening do not providea straightforward means of also determining the nature of theinteraction between a binding ligand and the biomolecular target.Information such as the stoichiometry and binding affinity of theinteraction often needs to be ascertained from additional biochemicalassays, thus slowing down and increasing the cost of drug discovery. Itis often the case that binding of a drug or ligand to a biomoleculartarget, such as a nucleic acid, may lead to a change in conformation ofthe biomolecule to a different structure. This, too, may contribute toprotection of the biomolecule from cleavage.

The present invention provides convenient methods for determining thesite or sites on a biomolecular target where a binding ligand interacts.This is accomplished based on the knowledge that collisionally activateddissociation (CID or CAD) of a noncovalent, biomolecule-ligand complexmay be performed such that cleavage of the complex occurs only atexposed sites of the biomolecules. Thus cleavage sites present on thebiomolecule that are involved in binding with the ligand are protectedbecause of the increased structural order from the binding event duringCID. ESI-MS^(n) Spectra generated using this method, in the presence andabsence of a binding ligand (or drug), will reveal differentialfragmentation patterns due to ligand induced protection of cleavagesites. Comparison of the mass spectra generated in the presence andabsence of a binding ligand will, therefore, reveal the positions in thebiomolecular sequence where the interactions between ligand andbiomolecule are occurring.

These methods for determining the sites of interaction between a bindingligand and a biomolecular target are broadly applicable. Thebiomolecular targets that may be studied using this method include, butare not limited to, peptides, proteins, antibodies, oligonucleotides,RNA, DNA, other nucleic acids, glycopeptides, and oligosaccharides. Itis preferred that the biomolecular target be a nucleic acid. It isfurther preferred that the biomolecular target be a chimeric RNA/DNAnucleic acid, synthesized to selectively incorporate deoxynucleotides,(or other residues) in the sequence at specific locations. The bindingligand may be one of the groups of molecules including, but not limitedto, organic or inorganic, small to large molecular weight individualcompounds, mixtures and combinatorial libraries of ligands, inhibitors,agonists, antagonists, substrates, and biopolymers, such as peptides oroligonucleotides.

Determination of the sites on an RNA target where interaction occurswith a binding ligand may be accomplished as follows. An RNA target thatis to be studied as a biomolecular target is prepared using an automatedsynthesizer, and selectively incorporating deoxynucleotides into thesequence at specific sites. An aliquot of this RNA/DNA chimeric is useddirectly for ESI-MS, followed by CID analysis of selectively accumulatedions, to establish the native structure and cleavage patterns of thisbiomolecular target. A second aliquot of the RNA/DNA chimeric is mixedwith a solution of a drug or ligand that is known to bind to thebiomolecular target. The target and ligand are anticipated to interactin solution to form a noncovalent complex. Subjecting this solution ofthe noncovalent biomolecule-ligand complex to the method of thisinvention leads to ionization of the complex with a retention of thenoncovalent interactions and binding stoichiometries. CID of the complexthen leads to cleavage of the biomolecule sequence at fragmentationsites that are exposed. Sites where fragmentation would otherwise occur,but which are involved in binding the ligand to the biomolecule, areprotected, such that cleavage at or near these sites is prevented duringthe CID stage. The differences in the fragmentation patterns of thebiomolecule when, subjected to the methods of this invention in thepresence and absence of binding ligand indicate the site(s) on thebiomolecule that is protected and, therefore, are involved in bindingthe ligand.

Likewise, a systematic pattern of deoxynucleotide incorporation into thesequence of the test RNA will allow for a systematic mass spectrometricassessment of binding sites and interactions in a certain area of thenucleic acid, or for the entire nucleic acid, using the method of thisinvention. This invention, therefore, also provides a new method of‘footprinting’ biomolecular targets especially nucleic acids. Thisfootprinting by mass spectrometry is a straightforward method formapping the structure of biomolecular targets and the sites ofinteractions of ligands with these targets.

The nature of interactions between the binding ligand and a biomoleculartarget are also readily studied using the method of this invention.Thus, the stoichiometry and absolute and relative dissociation constantof the biomolecule-ligand noncovalent complex is readily ascertainedusing the method of this invention. The ratio of the number of ligandmolecules and the number of biomolecular receptors involved in theformation of a noncovalent biomolecule-ligand complex is of significantimportance to the biochemist and medicinal chemist. Likewise, thestrength of a noncovalent complex, or the binding affinity of the ligandfor the biomolecular target, is of significance because it provides anindication of the degree of complementarity between the ligand and thebiomolecule. Also, the determination of this binding affinity isimportant for the rank ordering of different ligands so as to providestructure-activity relationships for a series of ligands, and tofacilitate the design of stronger binding ligands for a particularbiomolecular target.

The methods of the present invention are also capable of determiningboth the binding stoichiometry and affinity of a ligand for thebiomolecular target being screened in a screening study. Electrosprayionization is known to retain to a significant degree, the solutionphase structures of biomolecules and their noncovalent complexes in thegaseous ions it generates. Thus, determination of the stoichiometry ofnoncovalent complexes simply needs data on the masses of the ligand,biomolecular target and the noncovalent biomolecule-ligand complex. Thedata needed to accomplish this determination is actually available fromthe mass spectrometry experiment that may be performed to determine thestructure and site of binding of a ligand to the biomolecular target.Based on the knowledge of the structure and sequence of the targetbiomolecule, MS analysis of the biomolecule-ligand complex reveals thenumber of ligand and target molecules present in the noncovalentcomplex. If the noncovalent complex ion observed from the mass spectrumis of an m/z equal to that expected from the addition of the m/z valuesof one molecule each of the target biomolecule and ligand, then thenoncovalent complex must be formed from a 1:1 interaction between thebiomolecule and ligand. Simple mathematical operations on the molecularweight and charges of the target and ligand can likewise determinehigher levels of interactions between ligand and biomolecule. The highresolution of a FTICR mass spectrometer allows direct identification ofthe bound ligand based on exact measurement of the molecular mass of thecomplex relative to unbound nucleic acid.

The use of mass spectrometry, in accordance with this invention canprovide information on not only the mass to charge ratio of ionsgenerated from a sample, but also the relative abundance of such ions.Under standardized experimental conditions, it is therefore possible tocompare the abundance of a noncovalent biomolecule-ligand complex ionwith the ion abundance of the noncovalent complex formed between abiomolecule and a standard molecule, such as a known substrate orinhibitor. Through this comparison, binding affinity of the ligand forthe biomolecule, relative to the known binding of a standard molecule,may be ascertained. In addition, the absolute binding affinity can alsobe determined.

Determination of the nature of the interaction of a ligand with abiomolecular target may be carried out as exemplified for the binding ofa small molecule ligand with a nucleic acid target. A chimeric RNA/DNAbiomolecular target whose binding to a test ligand is to be studied isfirst prepared via automated synthesis protocols. An aliquot of a knownconcentration of chimeric nucleic acid is treated with a knownconcentration and quantity of a standard compound that is known to bindthat nucleic acid, such as the aminoglycoside paromomycin which is knownto bind to the 16S A-site of RNA. ESI-MS, followed by CID of theparomomycin-nucleic acid complex, affords a control spectrum for theinteractions and complex. A second aliquot of the chimeric nucleic acidis next treated with a test ligand using quantities and concentrationssimilar to those used for the control experiment. Application of themethod of the invention to this nucleic acid-ligand noncovalent complexaffords a test spectrum that reveals the nature of thebiomolecule-ligand interaction. Analysis of the noncovalent nucleicacid-ligand complex based on the known molecular weights of the twocomponents of the complex allows the determination of the number ofnucleic acid molecules and ligands present in the complex. Further,comparison of the abundance of the nucleic acid-ligand complex ion withthe abundance of the ion generated from the e.g. paromomycin-nucleicacid complex (or complex with any other known interacting species)provides a convenient and direct estimate of the binding affinity of thetest ligand compared to the standard, paromomycin. Since the standard iswell characterized, its solution binding affinity should be known fromother experiments or literature sources. For example, paromomycin bindsto a test 27-mer RNA with a ˜1 μM affinity. Knowing the binding affinityof the test ligand relative to paromomycin from the MS experiment, it isnow possible to determine the micromolar binding affinity of the testligand for the nucleic acid target being studied. Relative bindingaffinity may also be measured by testing a standard compound and testligand simultaneously as in a mixture with the target biomolecule, in asingle test assay.

Another object of the present invention is to provide general methodsfor the screening of compounds for drug discovery. The inventionprovides methods for the screening of a wide variety of biomoleculartargets that include, but are not limited to, peptides, proteins,receptors, antibodies, oligonucleotides, RNA, DNA, RNA/DNA hybrids,nucleic acids, oligosaccharides, carbohydrates, and glycopeptides. Themolecules that may be screened by using the methods of this inventioninclude, but are not limited to, organic or inorganic, small to largemolecular weight individual compounds, mixtures and combinatoriallibraries of ligands, inhibitors, agonists, antagonists, substrates, andbiopolymers, such as peptides or oligonucleotides.

The primary challenge when screening large collections and mixtures ofcompounds is not in finding biologically relevant activities, for thishas been demonstrated in many different cases, but in identifying theactive components from such screens, and often from mixtures and poolsof compounds that are found to be active. One solution that has beenpracticed by the art-skilled in high throughput drug discovery is theiterative deconvolution of mixtures. Deconvolution essentially entailsthe resynthesis of that combinatorial pool or mixture that was found tobe active in screening against a target of interest. Resynthesis mayresult in the generation of a set of smaller pools or mixtures, or a setof individual compounds. Rescreening and iterative deconvolution areperformed until the individual compounds that are responsible for theactivity observed in the screens of the parent mixtures are isolated.

However, analytical techniques are limited in their ability toadequately handle the types of mixtures generated in combinatorialefforts. The similarity of members of combinatorial mixtures or pools,and the complexity of such mixtures, prohibit effective analyticalassessment until the mixtures have been deconvoluted into individualcompounds, or at the very least into pools of only a handful ofcomponents. While this process of deconvolution, involving resynthesis,rescreening and analysis, is very cumbersome and time-consuming, it isalso very costly. A general method that alleviates these problems byrapidly revealing active mixtures and identifying the active componentsof such mixtures is clearly needed to save time and money in the drugdiscovery process.

The present invention solves the need for a method to rapidly assess theactivity of combinatorial mixtures against a biomolecular target andalso identify the structure of the active components of such mixtures.This is exemplified by the screening of combinatorial mixtures forbinding to a nucleic acid target as follows. A chimeric RNA/DNA targetof known sequence is selected as the screening target based onbiological relevance. This chimeric nucleic acid target is prepared viaautomated synthesis. An aliquot of the nucleic acid is used at aconcentration of 10 μM and treated with e.q. paromomycin acetate at aconcentration of 150 nM. A sample of the mixture is analyzed by themethod of the invention to demonstrate binding of the paromomycin byobservation of the paromomycin-nucleic acid complex ion. Next, analiquot of this mixture is treated with a DMSO solution of acombinatorial mixture of compounds such that the final concentration ofeach component of the mixture is ˜150 nM. This sample is then subjectedto ESI-MS, and the mass spectrum monitored for the appearance of newsignals that correspond to new nucleic acid-ligand noncovalent complexesformed with components of the combinatorial library.

The relative dissociation constants of these new complexes aredetermined by comparing the abundance of these new ions with theabundance of the paromomycin-nucleic acid complex ion whose bindingaffinity for the target is known a priori. Algorithmic deconvolution ofthe new complex ions observed, while taking into account the masses ofthe target and the components of the combinatorial library, provides themolecular weights of the binding ligands present in the observednoncovalent complexes. Alternatively, the identity of the binding ligandmay also be determined by first isolating the newly observed complex ionusing a triple quadrupole ion-trap or an ion cyclotron resonance device(ICR) followed by conventional identification by mass spectrometryfragment analysis. For example, upon isolation, a noncovalent complexion is ‘heated’ or dissociated into the constituent ligand andbiomolecule ions. This MS/MS experiment then can be tuned to studyfragmentation of the ligand. This information provides direct evidenceof the structure of the bound ligand. This method of the presentinvention, therefore, provides both the identity and relative bindingaffinity of members of combinatorial or other mixtures of compounds thatbind to the nucleic acid target.

Not only does the present invention provide methods for thedetermination of the molecular weight and absolute and relative bindingaffinity of the binding components of a combinatorial or other mixtureof compounds, but it also provides valuable information about the siteof binding on the biomolecular target. Such information permits theidentification of compounds having particular biological activity andgives rise to useful drugs, veterinary drugs, agricultural chemicals,industrial chemicals, diagnostics and other useful compounds. This canalso be accomplished as part of the same mass spectrometric procedure byisolating the newly observed complex ions using a triple quadrupoleion-trap or an ion cyclotron resonance device (ICR). For example, uponisolation, a noncovalent complex ion is collisionally activated tocleave the chimeric nucleic acid target at exposed deoxynucleotidesites. This MS/MS procedure, then, can be tuned to study fragmentationof the biomolecular target.

Comparison of the cleavage and fragment patterns so obtained for thenucleic acid component of the noncovalent complex with patterns obtainedfor the native chimeric nucleic acid alone reveals the locations on thenucleic acid that are protected by the binding of the ligand. Thisindicates the binding sites for the ligand on the nucleic acid.Comparison of the cleavage patterns to those observed from the CID ofthe standard-nucleic acid complex ion provide correlations between thesites of binding of the new ligand and standard. In this fashion,ligands that bind to nucleic acid targets may be identified such thatthey compete for the same binding site on the nucleic acid where thestandard binds, or bind at completely different and new sites on thenucleic acid. Both these types of observations are of value from a drugdiscovery standpoint.

The methods of the present invention can be used to identify metal ionbinding sites on any of the biomolecules described herein. Preferably,the metal ion binding site binds alkali metals or alkaline earth metals.More preferably, the metal ions are Na⁺, Mg⁺⁺ and Mn⁺⁺.

Drug discovery, using any one of a number of different types ofbiomolecular targets attends use of the methods of this invention whichcan rapidly screen large combinatorial libraries and mixtures ofcompounds for binding activity against a specific target.

It is possible that combinatorial libraries and mixtures of compoundsbeing used for screening may contain components that are similar in massbecause their elemental compositions are similar while their structuresare different, or at the very least, isomeric or enantiomeric. In suchinstances, a simple algorithmic calculation of the molecular weight of abound ligand will be insufficient to provide the identity of the ligandfor there may be multiple components of the same molecular mass. Themethods of the invention are also capable of addressing and resolvingsuch problems of ligand identification. The use of MS/MS experiments tofurther fragment the bound ligand, following selective ion accumulationof the ligand ion from the noncovalent complex, is a simple techniquethat provides structural detail of the bound ligand. This mass andstructural information provided by the methods of this invention isexpected to resolve the vast majority of mass redundancy problemsassociated with the screening of large combinatorial libraries andmixtures of compounds.

In a preferred embodiment, the present invention also provides methodfor simultaneously screening multiple biomolecular targets againstcombinatorial libraries and mixtures or collections of compounds. Thisis a significant advantage of the present invention over currentstate-of-the-art techniques in the screening of compounds for suchbinding. There is believed to be no prior technique that allows thesimultaneous and rapid screening of multiple targets, while providingstructural detail on the target and binding ligand at the same time. Inaddition to providing methods for the rapid and simultaneous screeningof multiple biomolecular targets, the present invention also providesmethods for determining the structure and nature of binding of both thetarget and binding ligand.

As discussed above, mass spectrometry methods of the present inventionprovide a direct means for screening and identifying those components ofcombinatorial mixtures that bind to a target biomolecule in solution. Inorder to enhance efficiency, it is preferable to multiplex the screeningprocess by simultaneously screening multiple targets for bindingactivity against a combinatorial library or mixture of compounds. Thisstrategy is normally limited by the distribution of charge states andthe undesirable mass/charge overlap that will be generated from allpossible noncovalent biomolecule-ligand complexes that could be formedduring such a screening assay. This problem of overlapping peaks in themass spectra is further exacerbated if the biomolecular targets beingscreened are of similar sequence, composition, or molecular weight. Insuch instances it would not be possible to ascertain in a rapid andsimple operation the composition of biomolecule-ligand complexes becauseof the extensive mass redundancy present in the pool of biomoleculesbeing studied and possible in the combinatorial library being screened.

The method of the present invention alleviates the problem ofbiomolecular target mass redundancy through the use of special massmodifying molecular weight tags. These mass modifying tags are typicallyuncharged or positively charged groups such as, but not limited to,alkyl and tetraalkylammonium groups, and polymers such as, but notlimited to, polyethylene glycols (PEG), polypropylene, polystyrene,cellulose, sephadex, dextrans, cyclodextrins, peptides, andpolyacrylamides. These mass modifying tags may be selected based ontheir molecular weight contribution and their ionic nature. These massmodifying tags may be attached to the biopolymeric targets at one ormore sites including, but not limited to, the 2′—O—, 3′-terminus,5′-terminus or along the sugar-phosphate backbone of nucleic acidtargets. Addition of mass modifying tags to the 5′terminus of syntheticoligonucleotides can be realized either using conventionalphosphoramidite chemistry, other conventional chemistry or bybiochemical or enzymatic means. Such mass modification of a nucleic acidmay be carried out using conventional, manual or automated techniques.Alternatively, addition of mass modifying tags may be performed at the3′-terminus by the use of appropriately modified polymer or CPG supportsfor solid-phase synthesis of nucleic acids. Mass modification at the3′terminus may also be done by biochemical or enzymatic means. It isalso possible to attach mass modifying tags to the internucleotidelinkages of a nucleic acid. This may be performed via the use ofappropriately modified phosphoramidites, or other nucleoside buildingblocks during nucleic acid synthesis or via post-synthetic modificationof the internucleotide linkage. Further, attachment of mass modifyingtags to nucleic acid targets may also be accomplished via the use ofbifunctional linkers at any functional site on the nucleic acid.Similarly, when working with other classes of biomolecular targets thesemass modifying tags may likewise be incorporated at one or morepositions on the biomolecule. As will be apparent, inclusion in eithertarget or ligand of isotopic mass labels may also be useful.

Thus, similar nucleic acid and other biological targets may bedifferentially tagged for rapid mass spectrometric screening by themethods of this invention. When noncovalent complexes are observed fromthis multiplexed screening of multiple nucleic acid targets withmixtures of small molecular weight combinatorial libraries, theconstituent ligand and biomolecule are readily identified usingconventional mass analyzers such as quadrupole, ion trap, ICR, magneticsector, or TOF and followed by MS/MS. This is because the mass modifyingtags make the m/z (mass to charge ratio) of the signal arising from eachtarget biomolecule-ligand complex ion of similar charge, distinct in themass spectrum, and which results in cleanly separated ion peaks. Massredundancy and peak overlap are both avoided by the use of massmodifying tags.

The present invention is also highly useful in combination with othertechniques for the identification of ligands which interact withmolecular interaction sites on RNA and other nucleic acids. Molecularinteraction sites attend RNA and are believe to be highly important inthe functioning of such RNA. The nucleotide sequences of molecularinteraction sites are highly conserved, even among taxonomically diversespecies. Moreover, such molecular interaction sites have specificstructures which provide opportunities for ligand binding. Ascertainingwhich ligands bind to such sites as well as determining the relativeaffinities and specificities for the binding of each ligand provideslead compounds for drug discovery, therapeutics, agricultural chemistry,industrial chemistry and otherwise.

The present mass spectrometric techniques, especially the MASStechniques and those which possess similar analytical robustness andpower, are ideally suited for cooperating with drug and other discoveryand identification programs such as those which determine ligand bindingto molecular interaction sites. The identification of molecularinteraction sites in RNA and other nucleic acids and the determinationof hierarchies of molecular ligands which likely bind to such molecularinteraction sites can be evaluated through the present techniques. Thus,in accordance with preferred embodiments of the present invention, ahierarchy of ligands ranked in accordance with their anticipated orcalculated likelihood of binding to a molecular interaction site of anRNA are actually synthesized. Such synthesis is preferably accomplishedin an automated or robotized fashion, preferably from instruction setsprovided in attendance to the ranked hierarchy of ligands. The compoundsmay be prepared in a library or mixture since the present massspectrometric methods can evaluate pluralities of compounds and theircomplexes with RNA simultaneously.

After the ligands are synthesized, preferably in library form, they arecontacted with the RNA having the molecular interaction site ofinterest. Complexation or binding (conventionally, non-covalent binding)is permitted to occur. The complexed RNA—ligand library is then analyzedby mass spectrometry. A principal object of the analysis is preferablythe determination of which ligands bind to the RNA molecular interactionsite and, among those, which ones rank more highly in terms ofspecificity and affinity. Accordingly, it is possible to identify from amixture or library of compounds, which ones are the most interactivewith a particular molecular interaction site so as to be able tomodulate it. Such compounds can either be used themselves, or, morelikely, be used as lead compounds for modification into drugs,agricultural chemicals, environmental chemicals, industrial and foodchemicals and otherwise.

As described above, it is highly desirable to challenge RNAs havingmolecular interaction sites with libraries of compounds which havealready been predicted or calculated to be likely to interact with theinteraction sites. It is preferred that such molecules belong to rankedhierarchies so as to give rise to the greatest likelihood of findinghighly potent modulators of the target RNA.

While there are a number of ways to identify compounds likely tointeract with molecular interaction sites of RNA and other biologicalmolecules, preferred methodologies are described in U.S. patentapplications filed on even date herewith and assigned to the assignee ofthis invention. These application bear U.S. Serial Nos. (Unknown) andhave been assigned attorney docket numbers IBIS-0002, IBIS 0003,IBIS-0004, IBIS-0006 and IBIS-0007. All of the foregoing applicationsare incorporated by reference herein in their entirety.

One mass spectrometric method which is particularly useful when combinedwith the techniques of the foregoing commonly owned inventions providesthe determination of specificity and affinity of ligands to RNA targets.MASS (multi target affinity/specificity screening) techniques canprovide high throughput screening methods to analyze the specificity andaffinity of ligands to molecular interaction sites of nucleic acids,especially RNA. MASS employs high performance electrospray ionizationFourier transform ion cyclotron resonance mass spectrometry(ESI-FTICR-MS) to a) determine exact chemical composition of affinityselected ligands originating from a combinatorial library, b) determinerelative dissociation constants (Kd) of ligands complexed to thetarget(s), and c) determine the location of ligand binding. Thisinformation can be gathered from each target(s) or library set in asingle assay in less than 15 minutes. This scheme benefits from twounique aspects of the ESI-FTICR combination. The “soft” nature of theelectrospray ionization process allows specific noncovalent complexes tobe ionized and transferred into the gas phase intact where they areamenable to subsequent characterization by mass spectrometry. The highresolving power afforded by the FTICR platform facilitates thecharacterization of complex mixtures which, when combined with the highmass accuracy inherent to FTICR, provides unambiguous identification ofligands complexed with the molecular interaction site or sites of atarget or targets.

Binding site information can be obtained by comparing the gas phasefragmentation patterns of the free and complexed target and absolutebinding affinities while relative binding constants are derived from therelative abundance of complexes using a complex with a known Kd as aninternal standard. With knowledge of the specificity and affinity ofligands to the molecular interaction site of a target RNA, the desiredlead or ultimate compound for modulation of the RNA can be determined.Therapeutic, agricultural chemical, industrial chemical and otherproducts which benefit from modulation of such RNA attend this result.

The simultaneous screening of a combinatorial library of molecules ofmass 700-750, against two nucleic acid targets of the same molecularweight but different sequence, is demonstrated by the use of massmodifying tags. If both nucleic acids targets being studied are 27-merRNAs of mass 8927, then screening a library of molecules of mass 700-750could afford a bewildering jumble of noncovalent complex ions in themass spectrum of the mixture of the two nucleic acids and the library.However if one of the two targets is mass modified, for example by theuse of a PEG chain of mass 3575 attached at the 5′ terminus of thetarget, then the mass spectrum will be significantly simplified. It isknown that a 27-mer will generate multiply-charged ion signals,following electrospray ionization, of mass/charge values 1486.8, 1784.4,and 2230.8 for the (M-6H)⁶⁻, (M-5H)⁵⁻, and the (M-4H)⁴⁻ charge states.Upon binding to small molecules of mass 700-750, the unmodifiedRNA-ligand complexes are anticipated to occur in the 1603.2-1611.6,1924.4-1934.4, and 2405.8-2418.3 m/z range. If the second nucleic acidtarget were not modified in any way, the signals from its complexeswould have occurred in the same regions. However, using the massmodified RNA, bearing the PEG chain of mass 3575, results in theobservation of the corresponding mass modified RNA-ligand complexes tooccur in the 2199-2207.4, 2639-2649 and 3299-3311 m/z range. Thus allsignals from the second mass modified nucleic acid would be cleanlyresolved from those of the first RNA. These noncovalent complex ions maybe selected e.g. by triple, quadrupole, ion trap or ICR techniques, andstudied further by MS/MS to afford detailed understanding of the sitesof ligand-RNA interaction, and the nature of these interactions, as hasbeen discussed above.

In a further embodiment, the methods of this invention are applicablefor the determination of the specificity of binding interactions betweena ligand and a biomolecular target. By simultaneously screening multiplebiomolecular targets with one or more compounds, using the methods ofthis invention, it is possible to ascertain whether a ligand bindsspecifically to only one target biomolecule, or whether the bindingobserved with the target is reproduced with control biomolecules aswell, and is therefore non-specific. This is an important distinction tobe made when screening large libraries and collections of compounds forbinding to biomolecular targets. It is desirable to quickly distinguishthose ligands that are selective or specific for the biomolecular targetof interest from those that are non-specific and bind to any and alltargets. From the standpoint of drug discovery, it is most often thecase that undesirable biological activities arise from theindiscriminate, non-specific binding of molecules to unrelatedbiomolecules. The present invention provides a valuable andstraightforward method for assessing the specificity of interactionsbetween a ligand and a panel of targets.

The use of mass modifying tags for the simultaneous screening ofmultiple biomolecular targets is applicable to the determination ofbinding specificity of a ligand as well. Mass modifying tags may be usedto differentiate several biomolecular targets that serve as a controlpanel for screening a combinatorial library of individual compoundsagainst a specific biomolecular target. When simultaneously screeningmultiple biomolecular targets using the mass spectrometric methods ofthis invention, it is necessary to ensure good separation of the ionsthat result from each target and its complex with the binding ligand.This peak overlap is easily eliminated by the facile introduction ofdifferent mass modifying tags onto the different biomolecular targetsbeing studied. A mixture of the biomolecular target and the controlpanel is mixed with the ligand being evaluated. This solution is thenionized by ESI-MS, and the noncovalent complex ions observed may bedirectly identified as having resulted from the binding of the ligand toa specific target from the several biomolecular targets present in themixture. In this way, a qualitative indication of specificity orselectivity of binding for the desired target versus the controlbiomolecules may be obtained. This selectivity may also be quantitatedthrough the use of appropriate standards of known binding affinity andcomparison of the ligand-biomolecule complex ion abundance to theabundance of the standard-biomolecule abundance. Further, details on thenature of the specific or non-specific interaction of the ligand withthe different biomolecules may also be obtained following ion-selectionand subsequent MS/MS experiments, as discussed above.

Likewise, it is also possible to determine the proportional binding of aligand to two or more biomolecular targets using the methods of thisinvention. Thus by the use-of appropriate mass modifying tags on thedifferent biomolecular targets, the different noncovalent complexesformed via differential binding of the ligand can be readilydistinguished in the mass spectrometer. Quantitation of the binding ispossible by measuring the abundance of these ions. Comparing therelative abundances of these ions provides a means to determine theproportional binding of the ligand to the different biomoleculartargets.

Yet another application of the methods of the present invention is todetermine the differential binding of ligands to biomolecular targets ofdifferent origin. When studying the binding of small molecule ligands toRNA targets, it is straightforward to distinguish between thenoncovalent ligand-RNA complexes generated from binding to the twodifferent RNA targets, even though both may be screened simultaneouslyas a mixture in the same assay. Further, it is also possible todetermine specificity and selectivity of the ligand for one versus theother RNA, and to determine the relative affinities of binding to eachRNA target.

The methods of the present invention are applicable to the study of awide variety of biomolecular targets that include, but are not limitedto, peptides, proteins, receptors, antibodies, oligonucleotides, RNA,DNA, RNA/DNA hybrids, nucleic acids, modified oligonucleotides,peptide-nucleic acids (PNAs), oligosaccharides, carbohydrates, andglycopeptides. Further these biomolecular targets may be synthetic orisolated from natural sources. Biomolecular targets of natural origininclude, but are not limited to, those obtained from microbial, plant,animal, viral or human materials, such as, but not limited to, cells,cell extracts, fluids, tissues and organs.

The molecules that may be screened by using the methods of thisinvention include, but are not limited to, organic or inorganic, smallto large molecular weight individual compounds, and combinatorialmixture or libraries of ligands, inhibitors, agonists, antagonists,substrates, and biopolymers, such as peptides or oligonucleotides.

Combinatorial mixtures include, but are not limited to, collections ofcompounds, and libraries of compounds. These mixtures may be generatedvia combinatorial synthesis of mixtures or via admixture of individualcompounds. Collections of compounds include, but are not limited to,sets of individual compounds or sets of mixtures or pools of compounds.These combinatorial libraries may be obtained from synthetic or fromnatural sources such as, for example to, microbial, plant, marine, viraland animal materials. Combinatorial libraries include at least abouttwenty compounds and as many as a thousands of individual compounds andpotentially even more. When combinatorial libraries are mixtures ofcompounds these mixtures typically contain from 20 to 5000 compoundspreferably from 50-1000, more preferably from 50-100. Combinations offrom 100-500 are useful as are mixtures having from 500-1000 individualspecies. Typically, members of combinatorial libraries have molecularweight less than about 5000 Da.

The mass spectrometry techniques that may be used in the methods of thisinvention include all of the techniques and systems described herein orare subsequently developed. Tandem techniques are also useful, includingcombinations of all of the foregoing and LC/MS. The mass spectrometersused in the methods of this invention may be a single quadrupole, triplequadrupole, magnetic sector, quadrupole ion trap, time-of-flightinstrument, and FTICR. Future modifications to mass spectrometry areexpected to give rise to improved techniques which may also be usefulherein.

In another embodiment of the present invention, binding of mixtures ofaminoglycosides can be measured simultaneously against multiple RNAtargets of identical length and similar (or identical) molecular weight.Addition of a neutral mass tag to one of the RNA targets shifts those toa higher mass/charge ratio, where complexes with small molecules can beidentified unambiguously. An appropriately placed neutral mass tag doesnot alter RNA-ligand binding. Preferably, this method is demonstratedwith model RNAs corresponding to the decoding region of the prokaryoticand eukaryotic small subunit rRNAs and a mixture of compounds, such as,for example, five aminoglycosides. In the examples set forth below,complexes are observed between the aminoglycoside library and theprokaryotic rRNA model, while no aminoglycoside was observed to bind tothe mass tagged eukaryotic rRNA model. The differential binding data isconsistent with the eukaryotic A-site rRNA having a differentconfirmation compared to the prokaryotic A-site that prevents entry andbinding of neomycin-class aminoglycosides. Mass spectrometric analysisof neutral mass-tagged macromolecular targets represents a new highthroughput screening paradigm in which the interaction of multipletargets against a collection of small molecules can be evaluated inparallel.

The preferred model system employed herein comprises a library comprisedof five 2-deoxystreptamine aminoglycoside antibiotics which have a rangeof binding affinities for the decoding sites of the prokaryotic andeukaryotic ribosomal RNA ranging from ˜28 nM to ˜1.5 mM. FIG. 24illustrates the secondary structures for the 27-nucleotide models of the16S and 18S rRNA decoding sites. These constructs consist of a 7 basepair stem structure containing a non-canonical U—U and apurine-adenosine mismatch base pair adjacent to a bulged adenosineresidue closed by a UUCG tetraloop. NMR studies of a complex between 16Sand paromomycin show that the RNA makes primary hydrogen bond,electrostatic, and stacking contacts with the aminoglycoside (Fourmy, etal., Science, 1996, 274, 1367-1371) and that paromomycin binds in themajor groove of the model A-site RNA within the pocket created by theA—A base pair and the single bulged adenine. The masses for the two RNAmodels differ by only 15.011 Da and the (M-5H⁺)⁵⁻ species of theseconstructs differ by only 3 m/z units. While the high resolutioncapabilities of the FTICR mass spectrometer can easily resolve thesespecies, mass spectra from a solution containing both RNAs arecomplicated by overlap among the signals from free RNA ions and theirsodium and potassium-adducted species.

Methods to increase the separation between the associated signals in themass spectra due to overlap among signals from RNAs 16S and 18S aredescribed herein. RNA targets modified with additional unchargedfunctional groups conjugated to their 5′-termini have been synthesized.Such a synthetic modification is referred to herein as a neutral masstag. The shift in mass, and concomitant m/z of a mass-taggedmacromolecule moves the family of signals produced by the tagged RNAinto a resolved region of the mass spectrum.

When simultaneously screening of untagged 16S and untagged 18S against acombinatorial library of small molecules, if a complex were observed at515.011 Da higher than 16S, it would not be possible to directlydetermine (without tandem MS methods) whether the complex correspondedto a ligand weighing 515.011 Da complexed to the 16S target or a ligandweighing 500.000 Daltons complexed to 185. Furthermore, becausepositively charged ligands can have non-specific interactions with RNAoligomers, it is often desirable to assay libraries for specific andnon-specific binding by screening against two or more RNA targetssimultaneously (e.g. a structured target sequence and an unstructuredcontrol sequence) in a single ESI-MS experiment. This multiplexadvantage can be further exploited in the RNA-drug discovery arena inwhich libraries are to be assayed against multiple RNA targets ofsimilar, or identical, mass. A single analysis in which 5 RNA targetsare screened against a combinatorial library of 200 componentsfacilitates the direct evaluation of 1000 RNA-ligand interactions fromthe acquisition of a single mass spectrum.

While the ability to shift the m/z range of closely relatedmacromolecules is highly desirable as described above, it is preferablydesired that the mass tag does not alter key physical properties of thetarget or the ligand binding properties. Preferably, an 18-atom mass tag(C₁₂H₂₅O₉) attached to the 5′-terminus of the RNA oligomer through aphosphodiester linkage can be employed. This mass tag has no appreciableaffect on oligonucleotide solubility, ionization efficiency, or UVabsorbance, and does not alter RNA-ligand binding. This latter attributeis evidenced by the data in FIG. 25 that illustrates the conserved ratioof free:bound RNA for the untagged and tagged RNA models of thebacterial decoding site under competitive binding conditions withparomomycin.

Aminoglycoside antibiotics inhibit bacterial growth by disruptingessential prokaryotic RNA-protein and RNA—RNA interactions. In vivo, atherapeutic effect is realized because paromomycin alters essential RNAinteractions in prokaryotes (by binding to the 16S A-site with highaffinity) but does appreciably disrupt the function of the eukaryoticRNA complexes (owing to the low affinity of paromomycin for the 18SA-site). A compound that binds both the 16S and 18S A-sites with similaraffinity would likely inhibit bacterial growth but might also havedeleterious cytotoxic effects in eukaryotic cells and would not make asuitable therapeutic agent. Thus, the 16S/18S model RNA system can servenot only as an interesting target for new generation antibiotics, but asa well characterized control for our mass spectrometry based RNA-ligandaffinity assay.

The ESI-FTICR mass spectrum depicted in FIG. 26 was acquired from a 10mM mixture of untagged 16S and tagged 18S in the presence of anequimolar mixture of five aminoglycosides. It is to be understood thatother biomolecules may be used in place of the aminoglycosides. Theaminoglycosides have been selected from two classes of2-deoxystreptamines: 4,5-disubstituted (paromomycin, and lividomycin),and 4,6-disubstituted (tobramycin, sisomicin, and bekanamycin), presentat 500 nM each. Complexes corresponding to 1:1 binding of individualaminoglycosides were observed between 16S and all members of theaminoglycoside mixture, with the apparent affinities estimated from theabundances of the respective complexes differing substantially. Signalintensities from the complexes with paromomycin (m/z 1925.572) andlividomycin (m/z 1954.790) are consistent with MS-measured dissociationconstants of 110 nM and 28 nM, respectively. The intensities of 16Scomplexes with tobramycin (m/z 1895.960), bekanamycin (m/z 1899.171),and sisomicin (m/z 1891.972) were reduced, consistent with solutiondissociation constants of 1.5 mM. Wang, et al., Biochemistry, 1997, 36,768-779. Hence, under these assay conditions, the MS-observed ionabundances reflect the solution dissociation constants. The inset inFIG. 26 demonstrates the ability to resolve the isotopic envelope foreach complex and allows mass differences to be calculated fromhomo-isotopic species, thus, measuring the difference in m/z between theRNA target and the RNA-ligand complex allows precise mass determinationof the ligand. The spectrum is calibrated using multiple isotope peaksof the (M-5H⁺)⁵⁻ and (M-4H⁺)⁴⁻ charge states of the free RNA as internalmass standards which brackets the m/z range in which complexes areobserved. The average mass measurement error obtained for the complexesin FIG. 26 is 2.1 ppm when m/z differences are measured between the mostabundant (4 ¹³C) isotope peak of 16S and each complex. This postcalibration scheme is easily automated which enables rapid, highprecision mass measurements of affinity selected ligands againstmultiple targets in a high throughput mode.

The enhanced affinity of lividomycin for 16S relative to the affinity ofparomomycin for 16S is interesting. While lividomycin is believed tobind to the 16S ribosomal subunit, the exact site of interaction has notbeen established. Lividomycin has two significant structural differencesfrom paromomycin. First, the additional mannopyranosyl ring couldgenerate new macromolecular contacts with the RNA. However, theorientation of paromomycin ring IV is disordered in the NMR-derivedstructure for the complex with 16S. In addition, a hydroxyl group onring I that makes a contact with A1492 is missing. The relatively highabundance of the 16S-lividomycin complex suggests that lividomycin bindsat or near the 16S A-site, and generates additional contacts thatenhance the binding affinity nearly 4-fold. Perhaps the most strikingfeature of the spectrum in FIG. 26 is the complete absence of complexesbetween 18S and paromomycin or lividomycin. This result suggests theremust be poor shape and electrostatic complementarity between the4,5-disubstituted 2-DOS class of aminoglycoside and the conservedarchitecture of the eukaryotic ribosomal decoding site.

Thus, according to the invention, RNA targets with similar (oridentical) molecular masses can be labeled with small neutral moleculesto measure binding between the targets and ligands using massspectrometry. By screening multiple targets against ligand mixturessimultaneously, the information content of the assay is enhanced,resulting in a dramatic reduction in the number of analyses required.Although the increased complexity of the multi-substrate/ligand mixturesplaces high demands on the mass analyzer, the methods described hereinfacilitate the simultaneous analysis of numerous targets under identicalsolution conditions and ligand concentrations, further enhancing thehigh-throughput nature of the screening strategy and allowing directcomparisons of binding affinities for closely related targets. Thisconcept of “rational” target design should also be applicable in studiesof proteins that differ in amino acid sequence.

EXAMPLES Example 1 Determining the Structure of a 27-mer RNACorresponding to the 16S rRNA A Site

In order to study the structure of the 27-mer RNA corresponding to the16S rRNA A site, of sequence 5′-GGC-GUC-ACA-CCU-UCG-GGU-GAA-GUC-GCC-3′(SEQ ID NO:1) a chimeric RNA/DNA molecule that incorporates threedeoxyadenosine (dA) residues at positions 7, 20 and 21 was preparedusing standard nucleic acid synthesis protocols on an automatedsynthesizer. This chimeric nucleic acid of sequence5′-GGC-GUC-dACA-CCU-UCG-GGU-GdAdA-GUC-GCC-3′ (SEQ ID NO:2) was injectedas a solution in water into an electrospray mass spectrometer.Electrospray ionization of the chimeric afforded a set of multiplycharged ions from which the ion corresponding to the (M-5H)⁵⁻ form ofthe nucleic acid was further studied by subjecting it to collisionallyinduced dissociation (CID). The ion was found to be cleaved by the CIDto afford three fragments of m/z 1006.1, 1162.8 and 1066.2. Thesefragments correspond to the w₇ ⁽²⁻⁾, w₈ ⁽²⁻⁾ and the a₇-B⁽²⁻⁾ fragmentsrespectively, that are formed by cleavage of the chimeric nucleic acidadjacent to each of the incorporated dA residues.

The observation that cleavage and fragmentation of the chimeric RNA/DNAhas occurred adjacent to all three dA sites indicates that the test RNAis not ordered around the locations where the dA residues wereincorporated. Therefore, the test RNA is not structured at the 7, 20 and21 positions.

A systematic series of chimeric RNA/DNA molecules is synthesized suchthat a variety of molecules, each incorporating deoxy residues atdifferent site(s) in the RNA. All such RNA/DNA members are comixed intoone solution. MS analysis, as described above, are conducted on thecomixture to provide a complete map or ‘footprint’ that indicates theresidues that are involved in secondary or tertiary structure and thoseresidues that are not involved in any structure. See FIG. 1.

Example 2 Determining the Binding Site for Paromomycin on a 27-mer RNAcorresponding to the 16S rRNA A Site

In order to study the binding of paromomycin to the RNA of example 1,the chimeric RNA/DNA molecule of example 1 was synthesized usingstandard automated nucleic acid synthesis protocols on an automatedsynthesizer. A sample of this nucleic acid was then subjected to ESIfollowed by CID in a mass spectrometer to afford the fragmentationpattern indicating a lack of structure at the sites of dA incorporation,as described in Example 1. This indicated the accessibility of these dAsites in the structure of the chimeric nucleic acid.

Next, another sample of the chimeric nucleic acid was treated with asolution of paromomycin and the resulting mixture analyzed by ESIfollowed by CID using a mass spectrometer. The electrospray ionizationwas found to produce a set of multiply charged ions that was differentfrom that observed for the nucleic acid alone. This was also indicativeof binding of the paromomycin to the chimeric nucleic acid, because ofthe increased mass of the observed ion complex. Further, there was alsoobserved, a shift in the distribution of the multiply charged ioncomplexes which reflected a change in the conformation of the nucleicacid in the paromomycin-nucleic acid complex into a more compactstructure.

Cleavage and fragmentation of the complex by CID afforded informationregarding the location of binding of the paromomycin to the chimericnucleic acid. CD was found to produce no fragmentation at the dA sitesin the nucleic acid. Thus paromomycin must bind at or near all three dAresidues. Paromomycin therefore is believed to bind to the dA bulge inthis RNA/DNA chimeric target, and induces a conformational change thatprotects all three dA residues from being cleaved during massspectrometry. See FIG. 2.

Example 3 Determining the Identity of Members of a Combinatorial Librarythat Bind to a Biomolecular Target

1 mL (0.6 O.D.) of a solution of a 27-mer RNA containing 3 dA residues(from Example 1) was diluted into 500 μL of 1:1 isopropanol:water andadjusted to provide a solution that was 150 mM in ammonium acetate, pH7.4 and wherein the RNA concentration was 10 mM. To this solution wasadded an aliquot of a solution of paromomycin acetate to a concentrationof 150 nM. This mixture was then subjected to ESI-MS and the ionizationof the nucleic acid and its complex monitored in the mass spectrum. Apeak corresponding to the (M-5H)⁵⁻ ion of the paromomycin-27mer complexis observed at an m/z value of 1907.6. As expected, excess 27-mer isalso observed in the mass spectrum as its (M-5H)⁵⁻ peak at about 1784.The mass spectrum confirms the formation of only a 1:1 complex at 1907.6(as would be expected from the addition of the masses of the 27-mer andparomomycin) and the absence of any bis complex that would be expectedto appear at an m/z of 2036.5.

To the mixture of the 27-mer RNA/DNA chimeric and paromomycin was nextadded 0.7 mL of a 10 μM stock solution of a combinatorial library suchthat the final concentration of each member of the combinatorial libraryin this mixture with 27-mer target was ˜150 nM. This mixture of the27-mer, paromomycin and combinatorial compounds was next infused into anESI-MS at a rate of 5 mL/min. and a total of 50 scans were summed (4microscans each), with 2 minutes of signal averaging, to afford the massspectrum of the mixture.

The ESI mass spectrum so obtained, shown in FIG. 3, demonstrated thepresence of new signals for the (M-5H)⁵⁻ ions at m/z values of 1897.8,1891.3 and 1884.4. Comparing these new signals to the ion peak for the27-mer alone the observed values of m/z of those members of thecombinatorial library that are binding to the target can be calculated.The masses of the binding members of the library were determined to be566.5, 534.5 and 482.5, respectively. Knowing the structure of thescaffold, and substituents used in the generation of this library, itwas possible to determine what substitution pattern (combination ofsubstituents) was present in the binding molecules.

It was determined that the species of m/z 482.5, 534.5 and 566.5 wouldbe the library members that bore the acetic acid +MPAC groups, thearomatic +piperidyl guanidine groups and the MPAC +guanidylethylamidegroups, respectively. In this manner, if the composition of thecombinatorial library is known a priori, then the identity of thebinding components is straightforward to elucidate.

The use of FTMS instrumentation in such a procedure enhances both thesensitivity and the accuracy of the method. With FTMS, this method isable to significantly decrease the chemical noise observed during theelectro spray mass spectrometry of these samples, thereby facilitatingthe detection of more binders that may be much weaker in their bindingaffinity. Further, using FTMS, the high resolution of the instrumentprovides accurate assessment of the mass of binding components of thecombinatorial library and therefore direct determination of the identityof these components if the structural make up of the library is known.

Example 4 Determining the Site of Binding for Members of a CombinatorialLibrary that Bind to a Biomolecular Target

The mixture of 27-mer RNA/DNA chimeric nucleic acid, as target, withparomomycin and the combinatorial library of compounds from Example 3was subjected to the same ESI-MS method as described in Example 3. TheESI spectrum from Example 2 showed new signals arising from thecomplexes formed from binding of library members to the target, at m/zvalues of 1897.8, 1891.3 and 1884.4. The paromomycin-27mer complex ionwas observed at an m/z of 1907.3.

Two complex ions were selected from this spectrum for further resolutionto determine the site of binding of their component ligands on the27-mer RNA/DNA chimeric. First, the ions at 1907.3, that correspond tothe paromomycin-27mer complex, were isolated via an ion-isolationprocedure and then subjected to CID. No cleavage was found to occur andno fragmentation was observed in the mass spectrum. This indicates thatthe paromomycin binds at or near in the bulged region of this nucleicacid where the three dA residues are present. Paromomycin thereforeprotects the dA residues in the complex from fragmentation by CID.

Similarly, the ions at m/z 1897.8, that correspond to the complex of alibrary member with the 27mer target, were isolated via an ion-isolationprocedure and then subjected to CID using the same conditions used forthe previous complex, and the data was averaged for 3 minutes. Theresulting mass spectrum (FIG. 4) revealed six major fragment ions at M/zvalues of 1005.8, 1065.6, 1162.8, 2341.1, 2406.3 and 2446.0. The threefragments at m/z 1005.8, 1065.6 and 1162.8 correspond to the w₆ ⁽²⁻⁾,a₇-B⁽²⁻⁾ and w₇ ⁽²⁻⁾ ions from the nucleic acid target. The three ionsat higher masses of 2341.1, 2406.3 and 2446.0 correspond to thea₂₀-B⁽³⁻⁾ ion+566 Da, w₂₁ ⁽³⁻⁾ ion+566 Da and the a₂₁-B⁽³⁻⁾ ion+566 Da.The data demonstrates at least two findings: first, since only thenucleic acid can be activated to give fragment ions in this ESI-CIDexperiment, the observation of new fragment ions indicates that the1897.8 ion peak results from a library member bound to the nucleic acidtarget. Second, the library member has a molecular weight of 566. Thislibrary member binds to the GCUU tetraloop or the four base pairs in thestem structure of the nucleic acid target (the RNA/DNA. chimericcorresponding to the 16S rRNA A site) and it does not bind to the bulgedA site or the 6-base pair stem that contains the U*U mismatch pair ofthe nucleic acid target.

Further detail on the binding site of the library member can be gainedby studying its interaction with and influence on fragmentation oftarget nucleic acid molecules where the positions of deoxynucleotideincorporation are different.

Example 5 Determining the Identity of a Member of a CombinatorialLibrary that Binds to a Biomolecular Target and the Location of Bindingto the Target

A 10 mM solution of the 27-mer RNA target, corresponding to the 16S rRNAA-site that contains 3 dA residues (from Example 1), in 100 mM ammoniumacetate at pH 7.4 was treated with a solution of paromomycin acetate andan aliquot of a DMSO solution of a second combinatorial library to bescreened. The amount of paromomycin added was adjusted to afford a finalconcentration of 150 nM. Likewise, the amount of DMSO solution of thelibrary that was added was adjusted so that the final concentration ofeach of the 216 member components of the library was ˜150 nM. Thesolution was infused into a Finnigan LCQ ion trap mass spectrometer andionized by electrospray. A range of 1000-3000 m/z was scanned for ionsof the nucleic acid target and its complexes generated from binding withparomomycin and members of the combinatorial library. Typically 200scans were averaged for 5 minutes. The ions from the nucleic acid targetwere observed at m/z 1784.4 for the (M-5H)⁵⁻ ion and 2230.8 for the(M-4H)⁴⁻ ion. The paromomycin-nucleic acid complex was also observed assignals of the (M-5H)⁵⁻ ion at m/z 1907.1 and the (M-4H)⁴⁻ ion at m/z2384.4 u.

Analysis of the spectrum for complexes of members of the combinatoriallibrary and the nucleic acid target revealed several new signals thatarise from the noncovalent binding of members of the library with thenucleic acid target. At least six signals for such noncovalent complexeswere observed in the mass spectrum. Of these the signal at the lowestm/z value was found to be a very strong binder to the nucleic acidtarget. Comparison of the abundance of this ligand-nucleic acid complexion with the abundance of the ion derived from the paromomycin-nucleicacid complex revealed a relative binding affinity (apparent K_(D)) thatwas similar to that for paromomycin.

MS/MS experiments, with ˜6 minutes of signal averaging, were alsoperformed on this complex to further establish the molecular weight ofthe bound ligand. A mass of 730.0±2 Da was determined, since theinstrument performance was accurate only to ±1.5 Da. Based on thisobserved mass of the bound ligand and the known structures of thescaffold and substituents used in generating the combinatorial library,the structure of the ligand was determined to bear either of threepossible combinations of substituents on the PAP5 scaffold. The MS/MSanalysis of this complex also revealed weak protection of the dAresidues of the hybrid RNA/DNA from CID cleavage. Observation offragments with mass increases of 730 Da showed that the molecule bindsto the upper stem-loop region of the rRNA target.

Example 6 Determining the Identity of Members of a Combinatorial Librarythat Bind to a Biomolecular Target and the Location of Binding to theTarget

A 10 mM solution of the 27-mer RNA target, corresponding to the 16S rRNAA-site that contains 3 dA residues (from Example 1), in 100 mM ammoniumacetate at pH 7.4 was treated with a solution of paromomycin acetate andan aliquot of a DMSO solution of a third combinatorial library to bescreened. The amount of paromomycin added was adjusted to afford a finalconcentration of 150 nM. Likewise, the amount of DMSO solution of thelibrary that was added was adjusted so that the final concentration ofeach of the 216 member components of the library was ˜150 nM. Thesolution was infused into a Finnigan LCQ ion trap mass spectrometer andionized by electrospray. A range of 1000-3000 m/z was scanned for ionsof the nucleic acid target and its complexes generated from binding withparomomycin and members of the combinatorial library. Typically 200scans were averaged for 5 minutes. The ions from the nucleic acid targetwere observed at m/z 1784.4 for the (M-5)⁵⁻ ion and 2230.8 for the(M-4H)⁴⁻ ion. The paromomycin-nucleic acid complex was also observed assignals of the (M-5H)⁵⁻ ion at m/z 1907.1 and the (M-4H)⁴⁻ ion at m/z2384.4 u.

Analysis of the spectrum for complexes of members of the combinatoriallibrary and the nucleic acid target revealed several new signals thatarise from the noncovalent binding of members of the library with thenucleic acid target. At least two major signals for such noncovalentcomplexes were observed in the mass spectrum. MS/MS experiments, with ˜6minutes of signal averaging, were also performed on these two complexesto further establish the molecular weights of the bound ligands.

The first complex was found to arise from the binding of a molecule ofmass 720.2±2 Da to the target. Two possible structures were deduced forthis member of the combinatorial library based on the structure of thescaffold and substituents used to build the library. These include astructure of mass 720.4 and a structure of mass 721.1. MS/MS experimentson this ligand-target complex ion using CID demonstrated strongprotection of the A residues in the bulge structure of the target.Therefore this ligand must bind strongly to the bulged dA residues ofthe RNA/DNA target.

The second major complex observed from the screening of this library wasfound to arise from the binding of a molecule of mass 665.2±2 Da to thetarget. Two possible structures were deduced for this member of thelibrary based on the structure of the scaffold and substituents used tobuild the library. MS/MS experiments on this ligand-target complex ionusing CID demonstrated strong fragmentation of the target. Thereforethis ligand must not bind strongly to the bulged dA residues of theRNA/DNA target. Instead the fragmentation pattern, together with theobservation of added mass bound to fragments from the loop portion ofthe target, suggest See FIG. 6. that this ligand must bind to residuesin the loop region of the RNA/DNA target.

Example 7 Simultaneous Screening of a Combinatorial Library of Compoundsagainst Two Nucleic Acid Targets

The two RNA targets to be screened are synthesized using automatednucleic acid synthesizers. The first target (A) is the 27-mer RNAcorresponding to the 16S rRNA A site and contains 3 dA residues, as inExample 1. The second target (B) is the 27-mer RNA bearing 3 dAresidues, and is of identical base composition but completely scrambledsequence compared to target (A). Target (B) is modified in the last stepof automated synthesis by the addition of a mass modifying tag, apolyethylene glycol (PEG) phosphoramidite to its 5′-terminus. Thisresults in a mass increment of 3575 in target (B), which bears a massmodifying tag, compared to target (A).

A solution containing 10 mM target (A) and 10 mM mass modified target(B) is prepared by dissolving appropriate amounts of both targets into100 mM ammonium acetate at pH 7.4. This solution is treated with asolution of paromomycin acetate and an aliquot of a DMSO solution of thecombinatorial library to be screened. The amount of paromomycin added isadjusted to afford a final concentration of 150 nM. Likewise, the amountof DMSO solution of the library that is added is adjusted so that thefinal concentration of each of the 216 member components of the libraryis ˜150 nM. The library members are molecules with masses in the 700-750Da range. The solution is infused into a Finnigan LCQ ion trap massspectrometer and ionized by electrospray. A range of 1000-3000 m/z isscanned for ions of the nucleic acid target and its complexes generatedfrom binding with paromomycin and members of the combinatorial library.Typically 200 scans are averaged for 5 minutes.

The ions from the nucleic acid target (A) are observed at m/z 1486.8 forthe (M-6H)⁶⁻ ion, 1784.4 for the (M-5H)⁵⁻ ion and 2230.8 for the(M-4H)⁴⁻ ion. Signals from complexes of target (A) with members of thelibrary are expected to occur with m/z values in the 1603.2-1611.6,1924.4-1934.4 and 2405.8-2418.3 ranges.

Signals from complexes of the nucleic acid target (B), that bears a massmodifying PEG tag, with members of the combinatorial library areobserved with m/z values in the 2199-2207.4, 2639-2649 and 3299-3311ranges. Therefore, the signals of noncovalent complexes with target (B)are cleanly resolved from the signals of complexes arising from thefirst target (A). New signals observed in the mass spectrum aretherefore readily assigned as arising from binding of a library memberto either target (A) or target (B).

Extension of this mass modifying technique to larger numbers of targetsvia the use of unique, high molecular weight neutral and cationicpolymers allows for the simultaneous screening of more than two targetsagainst individual compounds or combinatorial libraries.

Example 8 Simultaneous Screening of a Combinatorial Library of Compoundsagainst Two Peptide Targets

The two peptide targets to be screened are synthesized using automatedpeptide synthesizers. The first target (A) is a 27-mer polypeptide ofknown sequence. The second target (B) is also a 27-mer polypeptide thatis of identical amino acid composition but completely scrambled sequencecompared to target (A). Target (B) is modified in the last step ofautomated synthesis by the addition of a mass modifying tag, apolyethylene glycol (PEG) chloroformate to its amino terminus. Thisresults in a mass increment of ˜3600 in target (B), which bears a massmodifying tag, compared to target (A).

A solution containing 10 mM target (A) and 10 mM mass modified target(B) is prepared by dissolving appropriate amounts of both targets into100 mM ammonium acetate at pH 7.4. This solution is treated an aliquotof a DMSO solution of the combinatorial library to be screened. Theamount of DMSO solution of the library that is added is adjusted so thatthe final concentration of each of the 216 member components of thelibrary is ˜150 nM. The library members are molecules with masses in the700-750 Darange. The solution is infused into a Finnigan LCQ ion trapmass spectrometer and ionized by electrospray. A range of 1000-3000 m/zis scanned for ions of the polypeptide target and its complexesgenerated from binding with members of the combinatorial library.Typically 200 scans are averaged for 5 minutes.

The ions from the polypeptide target (A) and complexes of target (A)with members of the library are expected to occur at much lower m/zvalues that the signals from the polypeptide target (B), that bears amass modifying PEG tag, and its complexes with members of thecombinatorial library Therefore, the signals of noncovalent complexeswith target (B) are cleanly resolved from the signals of complexesarising from the first target (A). New signals observed in the massspectrum are therefore readily assigned as arising from binding of alibrary member to either target (A) or target (B). In this fashion, twoor more peptide targets may be readily screened for binding against anindividual compound or combinatorial library.

Example 9 Gas-phase Dissociation of Nucleic Acids for Determination ofStructure

Nucleic acid duplexes can be transferred from solution to the gas phaseas intact duplexes using electrospray ionization and detected using aFourier transform, ion trap, quadrupole, time-of-flight, or magneticsector mass spectrometer. The ions corresponding to a single chargestate of the duplex can be isolated via resonance ejection,off-resonance excitation or similar methods known to those familiar inthe art of mass spectrometry. Once isolated, these ions can be activatedenergetically via blackbody irradiation, infrared multiphotondissociation, or collisional activation. This activation leads todissociation of glycosidic bonds and the phosphate backbone, producingtwo series of fragment ions, called the w-series (having an intact3′-terminus and a 5′-phosphate following internal cleavage) and thea-Base series (having an intact 5′-terminus and a 3′-furan). Theseproduct ions can be identified by measurement of their mass/charge ratioin an MS/MS experiment.

An example of the power of this method is presented in FIGS. 8 and 9.Shown in FIG. 8 part A is a graphical representation of the abundancesof the w and a-Base ions resulting from collisional activation of the(M-5H)⁵⁻ ions from a DNA:DNA duplex containing a G—G mismatch base pair.The w series ions are highlighted in black and point toward the duplex,while the a-Base series ions are highlighted in gray and point away fromthe duplex. The more abundant the fragment ion, the longer and thickerthe respective arrow. Substantial fragmentation is observed in bothstrands adjacent to the mismatched base pair. The results obtainedfollowing collisional activation of the control DNA:DNA duplex ion isshown in FIG. 8 part B. Some product ions are common, but the pattern offragmentation differs significantly from the duplex containing themismatched base pair. Analysis of the fragment ions and the pattern offragmentation allows the location of the mismatched base pair to beidentified unambiguously. In addition, the results suggest that the gasphase structure of the duplex DNA ion is altered

by the presence of the mismatched pair in a way which facilitatesfragmentation following activation.

A second series of experiments with three DNA:RNA duplexes are presentedin FIG. 9 In the upper figure, an A-C mismatched pair has beenincorporated into the duplex. Extensive fragmentation producing w anda-Base ions is observed adjacent to the mismatched pair. However, theincreased strength of the glycosidic bond in RNA limits thefragmentation of the RNA strand. Hence, the fragmentation is focusedonto the DNA strand. In the central figure, a C—C mismatched base pairhas been incorporated into the duplex, and enhanced fragmentation isobserved at the site of the mismatched pair. As above, fragmentation ofthe RNA strand is reduced relative to the DNA strand. The lower figurecontains the fragmentation observed for the control RNA:DNA duplexcontaining all complementary base pairs. A common fragmentation patternis observed between the G5-T4 bases in all three cases. However, theextent of fragmentation is reduced in the complementary duplexesrelative to the duplexes containing base pair mismatches.

Example 10 MASS Analysis of RNA—Ligand Complex to Determine Binding ofLigand to Molecular Interaction Site

The ability to discern through mass spectroscopy whether or not aproposed ligand binds to a molecular interaction site of an RNA can beshown. FIGS. 10 and 11 depict the mass spectroscopy of an RNA segmenthaving a stem-loop structure with a ligand, schematically illustrated byan unknown, functionalized molecule. The ligand is combined with the RNAfragment under conditions selected to facilitate binding and the resultin complex is analyzed by a multi target affinity/specificity screening(MASS) protocol. This preferably employs electrospray ionization Fouriertransform ion cyclotron resonance mass spectrometry as describedhereinbefore and in the references cited herein. “Mass chromatography”as described above permits one to focus upon one bimolecular complex andto study the fragmentation of that one complex into characteristic ions.The situs of binding of ligand to RNA can, thus, be determined throughthe assessment of such fragments; the presence of fragmentscorresponding to molecular interaction site and ligand indicating thebinding of that ligand to that molecular interaction site.

FIG. 10 depicts a MASS Analysis of a Binding Location for a non-A SiteBinding molecule. The isolation through “mass chromatography” andsubsequent dissociation of the (M-5H)5− complex is observed at m/z1919.8. The mass shift observed in select fragments relative to thefragmentation observed for the free RNA provides information about wherethe ligand is bound. The (2−) fragments observed below m/z 1200correspond to the stem structure of the RNA; these fragments are notmass shifted upon Complexation. This is consistent with the ligand notbinding to the stem structure.

FIG. 11 shows a MASS Analysis of Binding Location for the non-A SiteBinding molecule. Isolation (i.e. “mass chromatography”) and subsequentdissociation of the (M-5H)5− complex observed at m/z 1929.4 providessignificant protection from fragmentation in the vicinity of the A-site.This is evidenced by the reduced abundance of the w and a-base fragmentions in the 2300-2500 m/z range. The mass shift observed in selectfragments relative to the fragmentation observed for the free RNAprovides information about where the ligand is bound. The exactmolecular mass of the RNA can act as an internal or intrinsic mass labelfor identification of molecules bound to the RNA. The (2-) fragmentsobserved below m/z 1200 correspond to the stem structure of the RNA.These fragments are not mass shifted upon Complexation—consistent withligand not being bound to the stem structure. Accordingly, the locationof binding of ligands to the RNA can be determined.

Example 11 Determination of Specificity and Affinity of Ligand Librariesto RNA Targets

A preferred first step of MASS screening involves mixing the RNA target(or targets) with a combinatorial library of ligands designed to bind toa specific site on the target molecule(s). Specific noncovalentcomplexes formed in solution between the target(s) and any librarymembers are transferred into the gas phase and ionized by ESI. Asdescribed herein, from the measured mass difference between the complexand the free target, the identity of the binding ligand can bedetermined. The dissociation constant of the complex can be determinedin two ways: if a ligand with a known binding affinity for the target isavailable, a relative Kd can be measured by using the known ligand as aninternal control and measuring the abundance of the unknown complex tothe abundance of the control, alternatively, if no internal control isavailable, Kd's can be determined by making a series of measurements atdifferent ligand concentrations and deriving a Kd value from the“titration” curve.

Because screening preferably employs large numbers of similar,preferably combinatorially derived, compounds, it is preferred that inaddition to determining whether something from the library binds thetarget, it is also determined which compound(s) are the ones which bindto the target. With highly precise mass measurements, the mass identityof an unknown ligand can be constrained to a unique elementalcomposition. This unique mass is referred to as the compound's“intrinsic mass label.” For example, while there are a large number ofelemental compositions which result in a molecular weight ofapproximately 615 Da, there is only one elemental composition(C₂₃H₄₅N₅O₁₄) consistent with a monoisotopic molecular weight of615.2963012 Da. For example, the mass of a ligand (paromomycin in thisexample) which is noncovalently bound to the 16S A-site was determinedto be 615.2969+0.0006 (mass measurement error of 1 ppm) using the freeRNA as an internal mass standard. A mass measurement error of 100 ppmdoes not allow unambiguous compound assignment and is consistent withnearly 400 elemental compositions containing only atoms of C, H, N, andO. The isotopic distributions shown in the expanded views are primarilya result of the natural incorporation of 13C atoms; because highperformance FTICR can easily resolve the 12C-13C mass difference we canuse each component of the isotopic cluster as an internal mass standard.Additionally, as the theoretical isotope distribution of the free RNAcan be accurately simulated, mass differences can be measured between“homoisotopic” species (in this example the mass difference is measuredbetween species containing four 13C atoms).

Once the identity of a binding ligand is determined, the complex isisolated in the gas phase (i.e. “mass chromatography”) and dissociated.By comparing the fragmentation patterns of the free target to that ofthe target complexed with a ligand, the ligand binding site can bedetermined. Dissociation of the complex is performed either bycollisional activated dissociation (CAD) in which fragmentation iseffected by high energy collisions with neutrals, or infraredmultiphoton dissociation (IRMPD) in which photons from a high power IRlaser cause fragmentation of the complex.

A 27-mer RNA containing the A-site of the 16S rRNA was chosen as atarget for validation experiments. See FIG. 12. The aminoglycosideparomomycin is known to bind to the unpaired adenosine residues with aKd of 200 nM and was used as an internal standard. The target was at aninitial concentration of 10 mM while the paromomycin and each of the 216library members were at an initial concentration of 150 nM. While thisexample was performed on a quadrupole ion trap which does not afford thehigh resolution or mass accuracy of the FTICR, it serves to illustratethe MASS concept. Molecular ions corresponding to the free RNA areobserved at m/z 1784.4 (M-5H+)5− and 2230.8 4 (M-4H+)4−. The signalsfrom the RNA-paromomycin internal control are observed at m/z 1907.1 4(M-5H+)5− and 2384.4 4 (M-4H+)4−. In addition to the expectedparomomycin complex, a number of complexes are observed corresponding tobinding of library members to the target. See FIG. 13.

One member of this library (MW=675.8+1.5) forms a strong complex withthe target but MS/MS studies reveal that the ligand does not offerprotection of A-site fragmentation and therefore binds to the loopregion. Another member of Isis 113069 having an approximate mass of743.8+1.5 demonstrates strong binding to the target and, as evidenced byMS/MS experiments provides protection of the unpaired A residues,consistent with binding at the A-site.

The rapid and parallel nature of the MASS approach allows large numbersof compounds to be screened against multiple targets simultaneously,resulting in greatly enhanced sample throughput and information content.In a single assay requiring less than 15 minutes, MASS can screen 10targets against a library containing over 500 components and report backwhich compounds bind to which targets, where they bind, and with whatbinding affinity.

Example 12 High Precision ESI-FTICR Mass Measurement of 16S A SiteRNA/Paromomycin Complex

Electrospray ionization Fourier transform ion cyclotron resonance massspectrometry was performed on a solution containing 5 mM 16S RNA (the27-mer construct shown in FIG. 24) and 500 nM paromomycin is depicted inFIG. 13. A 1:1 complex was observed between the paromomycin and the RNAconsistent with specific aminoglycoside binding at the A-site. Theinsets show the measured and calculated isotope envelopes of the(M-5H+)5− species of the free RNA and the RNA-paromomycin complex. Highprecision mass measurements were acquired using isotope peaks of the(M-5H+)⁵⁻ and (M-4H⁺)⁴⁻ charge states of the free RNA as internal massstandards and measuring the m/z difference between the free and boundRNA.

Example 13 Mass of 60-Member Library Against 16S A-Site RNA

FTMS spectrum was obtained from a mixture of a 16S RNA model (10 mM) anda 60-member combinatorial library. Signals from complexes arehighlighted in the insert. Binding of a combinatorial library containing60 members to the 16S RNA model have been examined under conditionswhere each library member was present at 5-fold excess over the RNA. Asshown in FIG. 14, complexes between the 16S RNA and ˜5 ligands in thelibrary were observed.

An expanded view of the 1863 complex from FIG. 14 is shown in FIG. 15.Two of the compounds in the library had a nominal mass of 398.1 Da.Their calculated molecular weights based on molecular formulas indicatethat they differ in mass by 46 mDa. Accurate measurement of themolecular mass for the respective monoisotopic (all ¹²C, ¹⁴N, and 16O)[M-5H]⁵− species of the complex (m/z 1863.748) and the free RNA (m/z1784.126) allowed the mass of the ligand to be calculated as398.110±0.009 Da.

FIG. 16 shows high resolution ESI-FTICR spectrum of the library used inFIGS. 14 and 15, demonstrating that both library members with a nominalmolecular weight of 398.1 were present in the synthesized library.

Example 14 Compound Identification From a 60-Member CombinatorialLibrary with MASS

Based on the high precision mass measurement of the complex, the mass ofthe binding ligand was determined to be consistent with the librarymember having a chemical formula of C₁₅H₁₆N₄O₂F₆ and a molecular weightof 398.117 Da (FIG. 17). Thus, the identity of the binding ligand wasunambiguously established.

Example 15 Elemental Composition Constraints

Use of exact mass measurements and elemental constraints can be used todetermine the elemental composition of an “unknown” binding ligand.General constraints on the type and number of atoms in an unknownmolecule, along with a high precision mass measurement, allowdetermination of a limited list of molecular formulas which areconsistent with the measured mass. Referring to FIG. 18, the elementalcomposition is limited to atoms of C, H, N, and O and furtherconstrained by the elemental composition of a “known” moiety of themolecule. Based on these constraints, the enormous number of atomiccombinations which result in a molecular weight of 615.2969±0.0006 arereduced to two possibilities. In addition to unambiguously identifyingintended library members, this technique allows one skilled in the artto identify unintended synthetic by-products which bind to the moleculartarget.

Example 16 Determination Of The MASS K_(d) For 16S-Paromomycin

The results of direct determination of solution phase dissociationconstants (Kd's) by mass spectrometry is shown in FIG. 19. ESI-MSmeasurements of a solution containing a fixed concentration of RNA atdifferent concentrations of ligand were obtained. By measuring the ratioof bound:unbound RNA at varying ligand concentrations, the Kd wasdetermined by 1/slope of the “titration curve”. The MS derived value of110 nM is in good agreement with previously reported literature value of200 nM.

Example 17 Multi-target Affinity/Specificity Screening

A schematic representation for the determination of ligand binding siteby tandem mass spectrometry is shown in FIG. 20. A solution containingthe molecular target or targets is mixed with a library of ligands andgiven the opportunity to form noncovalent complexes in solution. Thesenoncovalent complexes are mass analyzed. The noncovalent complexes aresubsequently dissociated in the gas phase via IRMPD or CAD. A comparisonof the fragment ions formed from dissociation of the complex with thefragment ions formed from dissociation of the free RNA reveals theligand binding site.

Example 18 MASS Analysis of 27-Member Library with 16S A-Site RNA

FIG. 21 shows MASS screening of a 27 member library against a 27-mer RNAconstruct representing the prokaryotic 16S A-site. The inset revealsthat a number of compounds formed complexes with the 16S A-site.

Example 19 MASS Protection Assay

MS/MS of a 27-mer RNA construct representing the prokaryotic 16S A-sitecontaining deoxyadenosine residues at the paromomycin binding site isshown in FIG. 22. The top spectrum was acquired by CAD of the [M-5H]5−ion (m/z 1783.6) from uncomplexed RNA and exhibits significantfragmentation at the deoxyadenosine residues. The bottom spectrum wasacquired from by CAD of the [M-5H]5− ion of the 16S-paromomycin complex(m/z 1907.5) under identical activation energy as employed in the topspectrum. No significant fragment ions are observed in the bottomspectrum consistent with protection of the binding site by the ligand.

Two combinatorial libraries containing 216 tetraazacyclophanes dissolvedin DMSO were mixed with a buffered solution containing 10 mM 16S RNA(see FIG. 24) such that each library member was present at 100 nM. Theresulting mass spectra, shown in FIG. 23 reveal >10 complexes between16S RNA and library members with the same nominal mass. MS-MS spectraobtained from a mixture of a 27-mer RNA construct representing theprokaryotic 16S A-site containing deoxyadenosine residues at theparomomycin binding and the 216 member combinatorial library. In the topspectrum, ions from the most abundant complex from the first library([M-5H];5− m/z 1919.0) were isolated and dissociated. Dissociation ofthis complex generates three fragment ions at m/z 1006.1, 1065.6, and1162.4 that result from cleavage at each dA residue. More intensesignals are observed at m/z 2378.9, 2443.1, and 2483.1. These ionscorrespond to the w21(3−), a20-B(3−), and a21-B(3−) fragments bound to alibrary member with a mass of 676.0±0.6 Da. The relative abundances ofthe fragment ions are similar to the pattern observed for uncomplexedRNA, but the masses of the ions from the lower stem and tetraloop areshifted by complexation with the ligand. This ligand offers littleprotection of the deoxyadenosine residues, and must bind to the lowerstem-loop. The library did not inhibit growth of bacteria. In the bottomspectrum, dissociation of the most abundant complex from a mixture of16S RNA and the second library having m/z 1934.3 with the samecollisional energy yields few fragment ions, the predominant signalsarising from intact complex and loss of neutral adenine. The reducedlevel of cleavage and loss of adenine for this complex is consistentwith binding of the ligand at the model A site region as doesparomomycin. The second library inhibits transcription/translation at 5mM, and has an MIC of 2-20 mM against E. coli(imp-) and S. pyogenes.

Example 20 Neutral Mass Tag of Eukaryotic and Prokaryotic A-Sites

FIG. 24 shows secondary structures of the 27 base RNA models used inthis work corresponding to the 18S (eukaryotic) and 16S (prokaryotic)A-sites. The base sequences differ in seven positions (bold), the netmass difference between the two constructs is only 15.011 Da. Mass tagswere covalently added to the 5′ terminus of the RNA constructs usingtradition phosphoramadite coupling chemistry.

Methodology to increase the separation between the associated signals inthe mass spectra was developed in view of the overlap among signals fromRNAs 16S and 18S. RNA targets modified with additional unchargedfunctional groups conjugated to their 5′-termini were synthesized. Sucha synthetic modification is referred to herein as a neutral mass tag.The shift in mass, and concomitant m/z, of a mass-tagged macromoleculemoves the family of signals produced by the tagged RNA into a resolvedregion of the mass spectrum. ESI-FTICR spectrum of a mixture of 27-baserepresentations of the 16S A-site with (7 mM) and without (1 mM) an 18atom neutral mass tag attached to the 5-terminus in the presence of 500nM paromomycin is shown in FIG. 25. The ratio between unbound RNA andthe RNA-paromomycin complex was equivalent for the 16S and 16S+tag RNAtargets demonstrating that the neutral mass tag does not have anappreciable effect on RNA-ligand binding.

Example 21 Simultaneous Screening of 16S A-Site And 18S A-Site ModelRNAs Against Aminoglycoside Mixture

Paromomycin, lividomycin (MW=761.354 Da), sisomicin (MW=447.269 Da),tobramycin (MW=467.2591 Da), and bekanamycin (MW=483.254 Da) wereobtained from Sigma (St. Louis, Mo.) and ICN (Costa Mesa, Calif.) andwere dissolved to generate 10 mM stock solutions. 2′ methoxy analogs ofRNA constructs representing the prokaryotic (16S) rRNA and eukaryotic(18S) rRNA A-site (FIG. 24) were synthesized in house and precipitatedtwice from 1 M ammonium acetate following deprotection with ammonia (pH8.5). The mass-tagged constructs contained an 18-atom mass tag(C₁₂H₂₅O₉) attached to the 5′-terminus of the RNA oligomer through aphosphodiester linkage.

All mass spectrometry experiments were performed using an Apex II 70eelectrospray ionization Fourier transform ion cyclotron resonance massspectrometer (Bruker Daltonics, Billerica) employing an activelyshielded 7 tesla superconducting magnet. RNA solutions were prepared in50 mM NH₄OAc (pH 7), mixed 1:1 v:v with isopropanol to aid desolvation,and infused at a rate of 1.5 mL/min using a syringe pump. Ions wereformed in a modified electrospray source (Analytica, Branford) employingan off axis, grounded electrospray probe positioned ca. 1.5 cm from themetalized terminus of the glass desolvation capillary biased at 5000 V.A counter-current flow of dry oxygen gas heated to 225° C. was employedto assist in the desolvation process. Ions were accumulated in anexternal ion reservoir comprised of an RF-only hexapole, a skimmer cone,and an auxiliary electrode for 1000 ms prior to transfer into thetrapped ion cell for mass analysis. Each spectrum was the result of thecoaddition of 16 transients comprised of 256 datapoints acquired over a90,909 kHz bandwidth resulting in a 700 ms detection interval. Allaspects of pulse sequence control, data acquisition, and postacquisition processing were performed using a Bruker Daltonicsdatastation running XMASS version 4.0 on a Silicon Graphics (San Jose,Calif.) R5000 computer.

Mass spectrometry experiments were performed in order to detect complexformation between a library containing five aminoglycosides (Sisomicin(Sis), Tobramycin (Tob), Bekanomycin (Bek), Paromomycin (PM), andLivodomycin (LV)) and two RNA targets simultaneously. Signals from the(M-5H+)⁵− charge states of free 16S and 18S RNAs are detected at m/z1801.515 and 1868.338, respectively. As shown in FIG. 26, the massspectrometric assay reproduces the known solution binding properties ofaminoglycosides to the 16S A site model and an 18S A site model with aneutral mass linker. Consistent with the higher binding affinity oftheses aminoglycosides for the 16S A-site relative to the 18S A-site,aminoglycoside complexes are observed only with the 16S rRNA target.Note the absence of l8S-paromomycin and 18S-lividomycin complexes, whichwould be observed at the m/z's indicated by the arrows. The insetdemonstrates the isotopic resolution of the complexes. Using multipleisotope peaks of the (M-5H+)⁵⁻ and (M-4H+)⁴⁻ charge states of the freeRNA as internal mass standards, the average mass measurement error ofthe complexes is 2.1 ppm. High affinity complexes were detected betweenthe 16S A site 27mer RNA and paromomycin and lividomycin, respectively.Weaker complexes were observed with sisomycin, tobramycin and bekamycin.No complexes were observed between any of the aminoglycosides and the18S A site model. Thus, this result validates the mass spectrometricassay for identifying compounds that will bind specifically to thetarget RNAs. No other type of high throughput assay can provideinformation on the specificity of binding for a compound to two RNAtargets simultaneously. The binding of lividomycin to the 16S A site hadbeen inferred from previous biochemical experiments. The massspectrometer has been used herein to measure a K_(D) of 28 nM forlividomycin and 110 nM for paromomycin to the 16S A site 27mer. Thesolution K_(D) for paromomycin has been estimated to be between 180 nMand 300 nM.

Example 22 Targeted Site-Specific Gas-Phase Cleavage ofOligoribonucleotides—Application in Mass Spectrometry-BasedIdentification of Ligand Binding Sites

Fragmentation of oligonucleotides is a complex process, but appearsrelated to the relative strengths of the glycosidic bonds. Thisobservation is exploited by incorporating deoxy-nucleotides selectivelyinto a chimeric 2′-O-methylribonucleotide model of the bacterial rRNA Asite region. Miyaguchi, et al., Nucl. Acids Res., 1996, 24, 3700-3706;Fourmy, et al., Science, 1996, 274, 1367-1371; and Fourmy, et al., JMol. Biol., 1998, 277, 333-345. During CAD, fragmentation is directed tothe more labile deoxynucleotide sites. The resulting CAD mass spectrumcontains a small subset of readily assigned complementary fragment ions.Binding of ligands near the deoxyadenosine residues inhibits the CADprocess, while complexation at remote sites does not affect dissociationand merely shifts the masses of specific fragment ions. These methodsare used to identify compounds from a combinatorial library thatpreferentially bind to the RNA model of the A site region.

The 27-mer model of a segment of the bacterial A site region has beenprepared as a full ribonucleotide (see FIG. 27, compound R), and as achimeric 2′-O-methylribonucleotide containing three deoxyadenosineresidues (see FIG. 27, compound C). RNAs R and C have been preparedusing conventional phosphoramidite chemistry on solid support.Phosphoramidites were purchased from Glen Research and used as 0.1 Msolutions in acetonitrile. RNA R was prepared following the proceduregiven in Wincott, et al., Nucl. Acids Res., 1995, 23, 2677-2684, thedisclosure of which is incorporated herein by reference in its entirety.RNA C was prepared using standard coupling cycles, deprotected, andprecipitated from 10 M NH₄OAc. The aminoglycoside paromomycin binds toboth R and C with kD values of 0.25 and 0.45 micromolar, respectively.The reported kD values are around 0.2 μM. Recht, et al., J. Mol. Biol.,1996, 262, 421-436, Wong, et al., Chem. Biol., 1998, 5, 397-406, andWang, et al., Biochemistry, 1997, 36, 768-779. Paromomycin has beenshown previously to bind in the major groove of the 27mer model RNA andinduce a conformational change, with contacts to A1408, G1494, andG1491. Miyaguchi, et al., Nucl. Acids Res., 1996, 24, 3700-3706; Fourmy,et al., Science, 1996, 274, 1367-1371; and Fourmy, et al, J. Mol. Biol.,1998, 277, 333-345.

The mass spectrum obtained from a 5 μM solution of C mixed with 125 nMparomomycin (FIG. 28A) contains [M-5H]5− ions from free C at m/z 1783.6and the [M-5H]5− ions of the paromomycin-C complex at m/z 1907.3. Massspectrometry experiments have been performed on an LCQ quadrupole iontrap mass spectrometer (Finnigan; San Jose, Calif.) operating in thenegative ionization mode. RNA and ligand were dissolved in a 150 mMammonium acetate buffer at pH 7.0 with isopropyl alcohol added (1:1 v:v)to assist the desolvation process. Parent ions have been isolated with a1.5 m/z window, and the AC voltage applied to the end caps was increaseduntil about 70% of the parent ion dissociates. The electrospray needlevoltage was adjusted to −3.5 kV, and spray was stabilized with a gaspressure of 50 psi (60:40 N2:02). The capillary interface was heated toa temperature of 180° C. The He gas pressure in the ion trap was 1mTorr. In MS-MS experiments, ions within a 1.5 Da window having thedesired m/z were selected via resonance ejection and stored with q) 0.2.The excitation RF voltage was applied to the end caps for 30 ms andincreased manually to 1.1 Vpp to minimize the intensity of the parention and to generate the highest abundance of fragment ions. A total of128 scans were summed over m/z 700-2700 following trapping for 100 ms.Signals from the [M-4H]4− ions of C and the complex are detected at m/z2229.8 and 2384.4, respectively. No signals are observed from morehighly charged ions as observed for samples denatured withtripropylamine. In analogy with studies of native and denaturedproteins, this is consistent with a more compact structure for C and theparomomycin complex. The CAD mass spectrum obtained from the [M-5H]5−ion of C is presented in FIG. 28B. Fragment ions are detected at m/z1005.6 (w6)2−, 1065.8 (a7-B)2−, 1162.6 (w7)2−, 1756.5 (M-Ad)5−, 2108.9(w21-Ad)3−, 2153.4 (a20-B)3−, 2217.8 (w21)3−, and 2258.3 (a21-B)3−.McLuckey, et al., J. Am. Soc. Mass Spectrum., 1992, 3, 60-70 andMcLuckey, et al., J. Am. Chem. Soc., 1993, 115, 12085-12095. Thesefragment ions all result from loss of adenine from the threedeoxyadenosine nucleotides, followed by cleavage of the 3′-C—O sugarbonds. The CAD mass spectrum for the [M-5H]5− ion of the complex betweenC and paromomycin obtained with the same activation energy is shown inFIG. 28C. No fragment ions are detected from strand cleavage at thedeoxyadenosine sites using identical dissociation conditions of FIG.28B. The change in fragmentation pattern observed upon binding ofparomomycin is consistent with a change in the local chargedistribution, conformation, or mobility of A1492, A1493, and A1408 thatprecludes collisional activation and dissociation of the nucleotide.

Two combinatorial libraries containing 216 tetraazacyclophanes dissolvedin DMSO were mixed with a buffered solution containing 10 μM C such thateach library member is present at 100 nM. The resulting mass spectrareveal >10 complexes between C and library members with the same nominalmass. Ions from the most abundant complex from the first library([M-5H];⁵⁻ m/z 1919.0) were isolated and dissociated. As shown in FIG.29A, dissociation of this complex generates three fragment ions at m/z1006.1, 1065.6, and 1162.4 that result from cleavage at each dA residue.More intense signals are observed at m/z 2378.9, 2443.1, and 2483.1.These ions correspond to the w₂₁ ⁽³⁻⁾, a₂₀-B⁽³⁻⁾, and a₂₁-B⁽³⁻⁾fragments bound to a library member with a mass of 676.0=0.6Da. Therelative abundances of the fragment ions are similar to the patternobserved for uncomplexed C, but the masses of the ions from the lowerstem and tetraloop are shifted by complexation with the ligand. Thisligand offers little protection of the deoxyadenosine residues, and mustbind to the lower stem-loop. The libraries have been synthesized from amixture of charged and aromatic functional groups, and are described aslibraries 25 and 23 in: An, et al., Bioorg. Med. Chem. Lett., 1998, inpress. Dissociation of the most abundant complex from a mixture of C andthe second library having m/z 1934.3 with the same collisional energy(FIG. 29B) yields few fragment ions, the predominant signals arisingfrom intact complex and loss of neutral adenine. The mass of the ligand(753.5 Da) is consistent with six possible compounds in the libraryhaving two combinations of functional groups. The reduced level ofcleavage and loss of adenine from this complex is consistent withbinding of the ligand at the model A site region as does paromomycin.The second library inhibits transcription/translation at 5 μm, and hasan MIC of 2-20 μM against E. coli (imp-) and S. pyogenes.

Mass spectrometry-based assays provide many advantages foridentification of complexes between RNA and small molecules. Allconstituents in the assay mixture carry an intrinsic mass label, and noadditional modifications with radioactive or fluorescent tags arerequired to detect the formation of complexes. The chemical compositionof the ligand can be ascertained from the measured molecular mass of thecomplex, allowing rapid deconvolution of libraries to identify leadsagainst an RNA target. Incorporation of deoxynucleotides into a chimericoligoribonicleotide generates a series of labile sites wherecollisionally-activated dissociation is favored. Binding of ligands atthe labile sites affords protection from CAD observed in MS-MSexperiments. This mass spectrometry-based protection methods of theinvention can be used to establish the binding sites for small moleculeligands without the need for additional chemical reagents orradiobabeling of the RNA. The methodology can also be used in DNAsequencing and identification of genomic defects.

In accordance with preferred embodiments of the present invention,enhanced accuracy of determination of binding between targetbiomolecules and putative ligands is desired. It has been found thatcertain mass spectrometric techniques can give rise to such enhancement.As will be appreciated, the target biomolecule will always be present inexcess in samples to be spectroscopically analyzed. The exactcomposition of such target will, similarly, be known. Accordingly, theisotopic abundances of the parent (and other) ions deriving from thetarget will be known to precision.

In accordance with preferred embodiments, mass spectrometric data iscollected from a sample comprising target biomolecule (or biomolecules)which has been contacted with one or more, preferably a mixture ofputative or trial ligands. Such a mixture of compounds may be quitecomplex as discussed elsewhere herein. The resulting mass spectrum willbe complex as well, however, the signals representative of the targetbiomolecule(s) will be easily identified. It is preferred that theisotopic peaks for the target molecule be identified and used tointernally calibrate the mass spectrometric data thus collected sincethe M/e for such peaks is known with precision. As a result, it becomespossible to determine the exact mass shift (with respect to the targetsignal) of peaks which represent complexes between the target andligands bound to it. Given the exact mass shifts, the exact molecularweights of said ligands may be determined. It is preferred that theexact molecular weights (usually to several decimal points of accuracy)be used to determine the identity of the ligands which have actuallybound to the target.

In accordance with other preferred embodiments, the informationcollected can be placed into a relational or other database, from whichfurther information concerning ligand binding to the target biomoleculecan be extracted. This is especially true when the binding affinities ofthe compounds found to bind to the target are determined and included inthe database. Compounds having relatively high binding affinities can beselected based upon such information contained in the database.

It is preferred that such data collection and database manipulation beachieved through a general purpose digital computer. An exemplarysoftware program has been created and used to identify the smallmolecules bound to an RNA target, calculate the binding constant, andwrite the results to a relational database. The program uses as input afile that lists the elemental formulas of the RNA and the smallmolecules which are present in the mixture under study, and theirconcentrations in the solution. The program first calculates theexpected isotopic peak distribution for the most abundant charge stateof each possible complex, then opens the raw FTMS results file. Theprogram performs a fast Fourier transform of the raw data, calibratesthe mass axis, and integrates the signals in the resulting spectrum suchas the exemplary spectrum shown in FIG. 30. The peaks in the spectrumare preferably identified via centroiding as shown in FIG. 31, areintegrated, and preferably stored in a database. An exemplary data fileis shown in FIG. 32). The expected and observed peaks are correlated,and the integrals converted into binding constants based on theintensity of an internal standard. The compound identity and bindingconstant data are written to a relational database. This approach allowslarge amounts of data that are generated by the mass spectrometer to beanalyzed without human intervention, which results in a significantsavings in time.

FIG. 30 depicts electrospray ionization Fourier transform ion cyclotronresonance mass spectrometry of a solution which is 5 mM in 16S RNA (Ibis16628) and 500 nM in the ligand Ibis 10019. The raw time-domain datasetis automatically apodized and zerofilled twice prior to Fouriertransformation. The spectrum is automatically post-calibrated usingmultiple isotope peaks of the (M-5H⁺)⁵⁻ and (M-4H⁺)⁴⁻ charge states ofthe free RNA as internal mass standards and measuring the m/z differencebetween the free and bound RNA. The isotope distribution of the free RNAis calculated a priori and the measured distribution is fit to thecalculated distribution to ensure that m/z differences are measuredbetween homoisotopic species (e.g. monoisotopic peaks or isotope peakscontaining 4 ¹³C atoms).

FIG. 31 shows isotope clusters observed in the m/z range whereRNA-ligand complexes are expected are further analyzed by peakcentroiding and integration. FIG. 32 depicts data tabulated and storedin a relational database. Peaks which correspond to complexes betweenthe RNA target and ligands are assigned and recorded in the database. Ifan internal affinity standard is employed, a relative Kd isautomatically calculated from the relative abundance of the standardcomplex and the unknown complex and recorded in the database. FIG. 33depicts a flow chart for one computer program for effectuating certainaspects of the present invention.

When computer controlled collection of the foregoing information isprovided and computer control of relational databases is employed, thepresent invention is capable of very high throughput analysis of massspectrometric binding information. Such control facilitates theidentification of ligands having high binding affinities for the targetbiomolecules. Thus, automation permits the automatic calculation of themass of the binding ligand or ligands, especially when the mass of thetarget is used for internal calibration purposes. From the precise massof the binding ligands, their identity may be determined in an automatedway. The dissociation constant for the ligand-target interaction mayalso be ascertained using either known Kd and abundance of a referencecomplex or by titration with multiple measurements at differenttarget/ligand ratios. Further, tandem mass spectrometric analyses may beperformed in an automated fashion such that the site of the smallmolecule, ligand, interaction with the target can be ascertained throughfragmentation analysis. Computer input and output from the relationaldatabase is, of course, preferred.

                   #             SEQUENCE LISTING<160> NUMBER OF SEQ ID NOS: 2 <210> SEQ ID NO 1 <211> LENGTH: 27<212> TYPE: RNA <213> ORGANISM: Artificial Sequence <220> FEATURE:<223> OTHER INFORMATION: Description of Artificial  #Sequence:      OLIGONUCLEOTIDE <400> SEQUENCE: 1ggcgucacac cuucggguga agucgcc           #                  #             27 <210> SEQ ID NO 2 <211> LENGTH: 27 <212> TYPE: RNA<213> ORGANISM: Artificial Sequence <220> FEATURE:<223> OTHER INFORMATION: Description of Artificial  #Sequence:      OLIGONUCLEOTIDE <400> SEQUENCE: 2ggcgucacac cuucggguga agucgcc           #                  #             27

What is claimed is:
 1. A method for determining three dimensionalstructure of a nucleic acid comprising: (a) providing a chimeric versionof said nucleic acid having at least one modified subunit in apreselected position of the chimera; (b) ionizing said nucleic acidhybrid in a mass spectrometer to provide one or more ions of saidchimera; (c) fragmenting at least one of said ions; (d) collectingfragmentation data from said fragmentation; and (e) relating saidfragmentation data to said three dimensional structure.
 2. The method ofclaim 1 wherein said relating of fragmentation data comprisesidentification of the fragmentation pattern of said ions.
 3. The methodof claim 1 wherein said three-dimensional structure comprises asecondary or tertiary structures.
 4. The method of claim 1 wherein saidthree dimensional structure comprises at least one mismatched base pair,loop, bulge, kink or stem structure.
 5. The method of claim 1 whereinsaid nucleic acid is RNA.
 6. The method of claim 5 wherein said nucleicacid corresponds to a 16S rRNA A-site.
 7. The method of claim 1 whereinsaid nucleic acid chimera comprises RNA having one or moredeoxynucleotides at said preselected positions.
 8. The method of claim 1wherein said chimera comprises RNA or DNA having a nucleic acid analogmoieties at said preselected positions.
 9. The method of claim 1 whereinsaid ionizing of said chimera is achieved through electrosprayionization, atmospheric pressure ionization or matrix-assisted laserdesorption ionization.
 10. The method of claim 1 wherein said ionfragmentation takes place within a mass spectrometer capable ofperforming quadrupole, triple quadrupole, magnetic sector, ion trap, ioncyclotron resonance or time-of-flight mass spectrometry.
 11. The methodof claim 1 wherein said ion fragmentation involves collision-induceddissociation.
 12. The method of claim 1 wherein said ion fragmentationinvolves infrared multiphoton dissociation.
 13. A method for identifyinga binding site for a ligand on a biomolecular target comprising: (a)collecting mass spectral fragmentation data for said biomoleculartarget; (b) providing a complex of said biomolecular target and saidbinding agent; (c) ionizing said complex in a mass spectrometer toprovide one or more ions of said complex; (d) fragmenting at least oneof said ions deriving from the complex; (e) collecting fragmentationdata from said fragmentation of the ions from the complex; and (f)relating the fragmentation data of the ions of the complex with thefragmentation data from the biomolecular target to determine said siteof binding.
 14. The method of claim 13 wherein said biomolecular targetis a nucleic acid.
 15. The method of claim 13 wherein said biomoleculartarget is RNA.
 16. The method of claim 15 wherein said RNA correspondsto a 16S rRNA A-site.
 17. The method of claim 14 wherein said nucleicacid includes at least one non-native nucleotide or nucleotide analog atpreselected positions thereof.
 18. The method of claim 17 comprising DNAat said preselected positions of an RNA.
 19. The method of claim 13wherein said biomolecular target is a peptide, protein, antibody,carbohydrate, oligosaccharide or glycopeptide.
 20. The method of claim13 wherein said biomolecular target is a nucleic acid moiety.
 21. Themethod of claim 13 wherein said mass spectral fragmentation data forsaid biomolecular target is provided by: (i) ionizing said biomoleculartarget in a mass spectrometer to provide one or more ions of saidbiomolecular target; and (ii) fragmenting in a mass spectrometer atleast one of said ions.
 22. The method of claim 13 wherein said ionizingof said complex is achieved through electrospray ionization, atmosphericpressure ionization or matrix-assisted laser desorption ionization. 23.The method of claim 13 wherein said ion fragmentation takes place withina mass spectrometer capable of performing quadrupole, triple quadrupole,magnetic sector, ion trap, ion cyclotron resonance or time-of-flightmass spectrometry.
 24. The method of claim 13 wherein said ionfragmentation involves collision-induced dissociation.
 25. The method ofclaim 13 wherein said ion fragmentation involves infrared multiphotondissociation.
 26. The method of claim 13 wherein said complex isprovided by combining together said biomolecular target and said bindingagent.
 27. A method for identifying a compound which binds to apreselected biomolecular target, said compound being present in amixture of compounds comprising: (a) providing a complex of saidbiomolecular target and a standard binding compound which binds to saidtarget under conditions effective to achieve said binding; (b) combiningwith said complex under competitive binding conditions the mixture ofcompounds; (c) ionizing said combination in a mass spectrometer toprovide a plurality of ions; (d) fragmenting at least one of said ionsin a mass spectrometer; (e) collecting mass spectral data for thefragmentation; and (f) relating said mass spectral data to the existenceand degree of competitive binding.
 28. The method of claim 27 whereinsaid biomolecular target is a nucleic acid.
 29. The method of claim 28wherein said nucleic acid is RNA.
 30. The method of claim 29 whereinsaid RNA includes one or more deoxynucleotides at preselected locationsthereof.
 31. The method of claim 27 wherein said biomolecular target isa peptide, protein, antibody, carbohydrate, oligosaccharide orglycopeptide.
 32. A method for identifying a compound which binds to apreselected biomolecular target, said compound being present in amixture of compounds comprising: (a) providing a complex of saidbiomolecular target and a standard compound which binds to said targetunder conditions effective to achieve said binding; (b) acquiringfragmentation data from the mass spectrometric analysis of the complex;(c) combining with a further portion of said complex under competitivebinding conditions the mixture of compounds; (d) ionizing saidcombination in a mass spectrometer to provide a plurality of ions; (e)fragmenting at least one of said ions in a mass spectrometer, (f)collecting mass spectral data for the fragmentation; and (g) relatingthe mass spectral data acquired in steps (b) and (f) to the existenceand degree of competitive binding of said compound.
 33. A method foridentifying binding sites of a biomolecular target for compounds from acombinatorial library comprising: (a) providing mass spectralfragmentation data for said biomolecular target; (b) providing a firstcomplex of said biomolecular target and a standard binding compoundwhich binds to said target; (c) combining with said first complex acombinatorial mixture of compounds; (d) ionizing in a mass spectrometersaid combination from step Ĉ to provide a plurality of ions for saidcombination; (e) fragmenting at least one of said ions in a massspectrometer to generate fragmentation data; (f) relating thefragmentation data collected for said biomolecular target and theionized combination from step (d) to afford said identification.
 34. Themethod of claim 33 wherein said mass spectral data for said biomoleculartarget and said combination are compared to identify said binding sites.35. The method of claim 33 wherein said biomolecular target is a nucleicacid.
 36. The method of claim 35 wherein said nucleic acid is RNA.
 37. Amethod for determining the nature and extent of binding of a ligand witha molecular interaction site of a biomolecule comprising contacting thebiomolecule with the ligand under conditions selected to promote bindingof the ligand to the molecular interaction site to give rise to acomplex of said biomolecule and the ligand; ionizing the complex in amass spectrometer; fragmenting the ionized complex; and determiningwhether the ligand binds to the molecular interaction site and, if so,determining the strength of binding of such ligand as compared to otherligands bound to said molecular interaction site.
 38. The method ofclaim 37 wherein said biomolecule is RNA.
 39. The method of claim 37wherein said ionization is electrospray ionization.
 40. The method ofclaim 37 wherein said ligand is part of a library of compounds and saidbinding takes place in the presence of other members of the library. 41.The method of claim 37 wherein said fragmentation comprises collisionalactivated dissociation or infrared multiphoton dissociation.
 42. Themethod of claim 37 wherein said determining comprises Fourier transformion cyclotron resonance mass spectroscopy.
 43. A method of identifyingchemical ligands which bind with high specificity and affinity to amolecular interaction site of an RNA comprising preparing a library ofligands in accordance with a ranked hierarchy of such ligands predictedor calculated to be bindable to the molecular interaction site;contacting the RNA with the ligand library under conditions selected topromote binding of the ligand library to the molecular interaction siteof the RNA to give rise to complexes of said RNA and the ligands of thelibrary; ionizing the complexes in a mass spectrometer; fragmenting theionized complexes; and determining whether the ligand of each suchcomplex binds to the molecular interaction site of the RNA and, if so,determining the strength of binding of such ligand as compared to thebinding strength of other ligands of the library.
 44. The method ofclaim 43 wherein said ionization is electrospray ionization.
 45. Themethod of claim 43 wherein said fragmentation comprises collisionalactivated dissociation or infrared multiphoton dissociation.
 46. Themethod of claim 43 wherein said determining comprises Fourier transformion cyclotron resonance mass spectroscopy.
 47. The method of claim 13wherein said binding site is a metal ion binding site.
 48. The method ofclaim 47 wherein said metal ion is an alkali metal or alkaline earthmetal.
 49. The method of claim 48 wherein said metal ion is selectedfrom the group consisting of Na⁺, Mg⁺⁺, and Mn⁺⁺.
 50. The method ofclaim 33 wherein said binding site is a metal ion binding site.
 51. Themethod of claim 50 wherein said metal ion is an alkali metal or alkalineearth metal.
 52. The method of claim 51 wherein said metal ion isselected from the group consisting of Na⁺, Mg⁺⁺, and Mn⁺⁺.
 53. Themethod of claim 13 further comprising determining the absolute bindingaffinity of at least one binding agent and biomolecular target.
 54. Themethod of claim 33 further comprising determining the absolute bindingaffinity of at least one binding agent and biomolecular target.
 55. Amethod for identifying in a chemical mixture of compounds which bind toa biomolecular target, comprising: (a) providing mass spectral data onthe ion abundances for a blend of the mixture and an excess of saidtarget; (b) calibrating the mass spectral data by reference to themultiple isotope peaks for the uncomplexed target; (c) determining theexact mass shill of mass spectral data representing a subset of saidcompounds complexed with said target to ascertain the exact molecularweight of said complexed compounds.
 56. The method of claim 55 furthercomprising: (d) identifying the compounds from among those comprisingthe chemical mixture by reference to their exact molecular weights. 57.The method of claim 56 further comprising establishing a relationaldatabase to hold information collected in said determining andidentifying steps.
 58. The method of claim 57 further comprisingdetermining the binding affinity of the compounds found to bind to saidtarget and including said binding affinity data in said database. 59.The method of claim 58 further comprising selecting from among saidcompounds found to bind to said target, those having relatively highbinding affinity.